This is from 時をかける少女:
理科実験室での事件があってから、２、３日、和子はからだ調子がおかしかった。
と、いってもべつにどこか悪いとでもないし、気分が悪いというほどのこともない。
In second phrase, it starts only by と. How it works? This construction have a name? Rules? I saw with で too, but now I can’t find an example. More than the meaning, I want the theory behind it.
といっても is a conjunction [Jisho entry]
So, perhaps other examples you encountered are similarly just part of a whole, or it indeed was just a single particle on its own.
Even if you didn’t take this as a set expression, you can just see it as と (quotation particle) plus いう in the て form, plus も.
Usually there’s some kind of usage of that particle you can apply to the previous sentence.
But why it has a comma between?
Style? Makes it sound like there’s a pause.
What a pain…
Ok, so, we are free to put commas anywhere, because they are just for artistic purposes? 
Grammatically, no. Stylistically? Absolutely. People do this in English all the time in casual writing (social media, texting, you get the idea). Grammar rules have times and places to be bent, and it just so happens that (in my experience, anyway) those occurrences tend to be more frequent in Japanese than English. Even in daily conversation you’ll see a lot of Japanese grammar rules bent, or even broken entirely.
@Micha-kun, it is definitely a pain, but there’s nothing we can do about it, really. I’m certain English has similar difficulties coming from almost any other language.
Japanese does not have nearly as strict of rules with regard to comma placement as English. You’ll see them in various places, often just based on how the writer thinks it improves readability. But here it was just for style. And if someone is writing a novel, they pretty much can do whatever they want.
Of course we can’t do anything, it’s just a pain to think every posible combination of grammar, even if there are commas. When to stop to look at posible combinations?
You have the same problem without commas, too. If I see 来てからというもの, my first guess isn’t „oh the whole thing must be a grammatical construct“.
You have infinite possible combinations there, too, and it is annoying to look up. It’s frustrating to realize that the thing you tried to deconstruct for 10 minutes actually has a completely separate entry in jisho, but there isn’t really a way to solve this.
At least you’ll learn something along the way, and maybe next time you’ll recognize the expression right away. 
I thought you literally meant the phrase had an entry in jisho. I thought I was going to learn a new phrase!
EDIT: Ahahah, found it :'D
Oh, while on the topic. What about sentences ending with を？
I unfortunately don’t have any examples under the hand, but I’ve seen it decently often. Is a verb implied? Is it suru?
It could be something like this: https://jisho.org/word/よい旅行を
That is, expressions. Same with 良い一日を.
I guess the する can be implied, as you say.
Other times, it can be that the subject is before the を, like:
見て下さい、この本を。
Stuff like that.
Or perhaps like this: https://jisho.org/search/良いお年を
An abbreviation of a longer expression, where something is implied, but not necessarily する.
I’m not sure about と, but で is a conjunction on its own. Jisho says it means “and then; so”.
That’s an answer I’m expecting 
Thank you @seanblue.
@Myria it’s the only good think about this, bloody nonstop learning.
Is it really that problematic though? I’m not disagreeing with you in that, yeah, sometimes, you can’t know what you don’t know. But, I just wanted to say to @Micha-kun and others like them: I think it’s fine for beginners (and non-beginners) to merely decompose the sentence and carry on reading. A lot of times, grammar elements have broad meanings, and then specific phrases acquire a specialised meaning, so you won’t be too far off.
といっても is totally transparent, but even in the case of てからというもの, even if you take てから as “since” and というもの as “the matter of” (some kind of weak thematisation, like a weak は), you’d get most of the meaning. You miss out on the idiomatic aspect, that maybe it’s more precisely the time/period since/after something, or that it’s usually directly adverbialised, but really, not that much IMHO… and actually none of that is made explicit in the JMdict entry either.
と at the beginning of a sentence followed by something that looks like いう? You know it’s likely a quoting particle before いう; it probably quotes whatever comes before, even if it’s a whole sentence with a period. で at the beginning of a sentence? It’s probably the gerund/te-form of だ, so you re-read the previous sentence as if it ended in て instead—it’s like how you can sometimes use だから instead of adding から to the previous sentence. And it’s similar to how in English we start sentences with conjunctions all the time: and, or, etc. Now and then, you’ll get tripped and things won’t make any sense, i.e., you see Xところが, think it’s “the place where X” marked with が and then nothing makes sense; in that case, yeah, tough luck. (There are quite a few of those noun+particle => phrasal conjunction, though, so you learn to spot the possibility.)
None of the above is perfect, and it’s just my two cents, anyway, but it’s good to keep your learning/reading in perspective.
I agree that you don’t have to know extremely specialized grammar and still be able to understand stuff well, I just wanted to make a point that commas are probably the least problematic in hindering your grammar search, since you can simply ignore them.
I didn’t want to discourage anyone in saying that there’s so much complicated grammar everywhere! Just that the problem of not knowing where to stop searching is not just limited to cases where confusing commas are used.
Maybe I can ignore them, but how I can use them if they can be “anywhere”? What rules are for commas when writing?
Well, I’d say commas are mostly used in places where you would naturally pause in a sentence.
Sometimes after は, but mostly after contrastive conjunctions like が, けど, ても, のに, or other conjunctions like から and ので. Also after a verb in 中止形.
Or simply in various places to make the sentence more easily understandable and less ambiguous. When you have longer sentences they simply break up the flow a little and make things easier to parse.
That’s actually also related to why commas weren’t really used that much historically in Japanese, because using them implied that the reader was stupid and wouldn’t understand you without the “help” of commas. Luckily we’re past that, and they’re used in various places to make stuff easier to read.
Also, I don’t know if there’s actual rules that you can learn, I simply picked these up while reading.
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