Definitions:
本来 : primarily
主に : mainly, primarily
In English, I always considered “mainly” and “primarily” adverbs to have the equivalent logic behind them, and have always used them interchangeably. But no J-dictionary I’ve looked at lists “mainly” for 本来 even though it feels like, in “mentalese”, that’s exactly what 本来 means.
Am I wrong? What’s the nuance to differentiate them such that any given word which means “primarily” cannot also mean “mainly”?
主に has the first kind of meaning whereas 本来 has the second one. So the “primarily” translation of 本来 refers to how something was originally - 本 often means the root / origin of something
So it was me being bad at my own language that’s been messing me up with these two Japanese words, haha. I never actually looked up the definition of “primary” because I assumed I knew the definition for all these decades. Indeed, the etymology confirms it even more something I wasn’t even cognizant of:
late Middle English (in the sense ‘original, not derivative’): from Latin primarius , from primus ‘first’.
I wonder if people who know Latin run into this problem significantly less often when learning new languages.
It helps to look at the Japanese definitions.
本来 means
１ もともとそうであること。元来。
２ それが当たり前であること。道理であること。
It’s a bit of a stretch to say that either of those should be thought of as “mainly.” But given how loose translations can be, I would say it’s not impossible to see a sentence that uses 本来 get translated with mainly. That’s more about how translations work than about 本来 itself though.
For comparison, here’s 主に, and you can see they’re pretty different.
主として。大部分。ほとんど。
Actually the main meaning of “primary” is “main”, or “most important”. I’ve personally almost never seen “primary” (or “primarily”) used as “happening or coming first”. Maybe I missed this meaning or it shifted over time, but it seems odd to me to use when it’s so easily (mainly) misinterpreted.
The fact that the Latin etymology points to “first” does not define the (primary :P) meaning of the word in English. A word’s meaning is how it is used in the target language. Even if Latin was one of my favorite subjects in school by the way.
But I had to look this up in multiple dictionaries to confirm this myself.
From the Merriam Webster dictionary (“primary”):
Oxford Learner’s Dictionary (main Oxford is not freely available):
The discussion was about “primarily” though, which is a different part of speech than “primary”. I don’t think the OP was asking about if “primary” was acceptable for 主に or 本来.
And it’s still true that 主に and 本来 are different kinds of “primarily” from each other.
EDIT: Ah, I see you’re responding to the OP’s later post where they also mentioned “primary” (erroneously?)
It’s (mostly) the same thing, primarily is the adverb of primary.
From Merriam Webster (“primarily”):
I’ve never seen the “originally” usage, and it seems odd to me when it can be misinterpreted with its (current) main meaning. Maybe I missed it.
I’m not saying the word doesn’t have the meaning, I’m saying it can be confusing within WK because the main meaning is “mainly” and this secondary meaning is rarely used.
And yes, I was primarily responding to comment #3 about the word coming from Latin primus ‘first’ 
Interestingly, Merriam Webster says the “First Known Use of primarily:
1601, in the meaning defined at sense 1 [mainly]” (citation needed I suppose)
You will have a lot of doubts like this as you use an English Japanese dictionary. But when you switch to a Japanese only one, almost all this will fade away. (It is a tough step, though.)
You will have some doubts but by then you can quickly look up the differences in Japanese, explained by Japanese people.
Definition 2 is used quite a bit as well. Perhaps you went to primary school when you were younger, or go see a primary care physician before you get directed to a specialist.
More broadly, you use primer before paint when you change your room color, or prime a pump before you start it. Or have studied the primordial gods of Greek mythology.
The ‘pri’ root has strong ‘first’ connotations. The first definition of ‘Primarily’ is probably a corruption of it’s original usage.
Yeah, good points, though maybe ‘prime’ is a bit different. But primary school or primary care, etc. - definitely. ‘primarily’ on the other hand… rarely I’d say
Which Japanese dictionary are these from? they seem surprisingly readable to me.
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