Haha, you know too much Japanese 
One alternative might be to ask the staff to add one of those shake-y messages: “sorry, this reading is correct but not the one we’re looking for”
I have this same problem when people post things like Genki exercises. I can think of a few answers that would fit but it depends on what the material expects.
I swear わがあるじ is the only thing Ranga from Tensura says so this one is very firmly ingrained.
Why is this? Is it slang or a more obscure term for master?
If i am guessing this might be honorofic way of saying or old idk
I mean, fair game, right?
I would also recommend emailing them. This is a completely valid reading.
EDIT:
I got super confused by 主, because I’ve seen this kanji like a million times and somehow thought that I had it on WaniKani as a standalone vocab item already, but I see it’s level 30.
I have the same exact problem when Genki exercises expect me to translate from English to Japanese. Sometimes I’ve no idea what kind of answer they want exactly .
From how I understand it, 主 and 主 are two different words, though they overlap somewhat in the meaning “master”. I can’t really comment further, but I don’t think it’s slang or obscurity, they seem to have different situations that fits each word better than the other. From Weblio:
It’s an antiquated term for “master” and a viable reading for the kanji.
The kind of word you’d find mostly only find in period fiction.
Decided to try it on a whim. But, like, c’mon WK, just give it to me.
Yeah I had the exact same thing happen some time ago and was a bit annoyed when it got marked wrong…then promptly forgot about it and never thought to email WK about it
It’s just a programming oversight. It’s a similar problem to ビー玉 accepting びーだま but rejecting びいだま. It’s a consequence of the fact that traditional software programming does exactly what you tell it to, and absolutely nothing more or less.
But if it’s two different words, and not just two spellings/readings for the same word, then AFAIK Wanikani can’t support both due to some technical difficulties. It’s the same case as with
I admit I’m not really sure what the back-end problem with including the multiple different kunyomi readings for bits of single-character vocab like 額 and 主 would be, with a shake if they don’t want to accept them as a pair with the English word they offer. They already do that for entering the wrong type of reading on the kanji answer prompt.
But particularly for 主, since あるじ and ぬし are near 1:1 in meaning and could be paired with the same English vocab.
(To clarify, it’s not a big deal and I’m not actually upset about this.)
Wait, that doesn’t take やいば?
Site literally unusable.
Yeah, right? I only just had it in vocab and was surprised to see not やいば but は.
It’s because, much like あるじ, it’s a word you’ll probably only ever encounter in historical fiction and fantasy.
I get them both not being the main answers, but …
I hear you 
I’ve begun to write the team every time I come across a situation like this, explaining when there are two readings, or because the on’yomi is being used for kanji that they should also allow the kun’yomi, or at least do the shake-thing when someone enters it (as I sometimes do) so I won’t fail the question, because my answer was right, just not what they were looking for. I make photos from my dictionaries and/or screenshots to corroborate, so they see I’m not just making things up. At least I spend more time on certain kanji/vocab and have extra exposure 
Back-end wise there shouldn’t be any problem, I believe. There are multiple vocab items with multiple readings so it’s just a matter of adding an extra one. Both words theoretically mean “master” and we have tons of other vocab items with overlapping meaning so this should be okay .
There is also at least one precedent for multiple meanings and readings in a single vocab item: 避ける, which the entry readily explains as さける = avoid and よける= dodge.