I've been wondering whether this will be a problem for me or not when I start reading native material. Basically in my core deck there are words with similar kanji but spelled differently depending on context.

For example (pardon the romaji) maitoshi/mainen(every year), myounichi/ashita/asu(tomorrow), hayari/ryuukou(fashion) etc.

So, how can I ever learn the correct spelling if there is no furigana and the words are similar?

I think it's a matter of guesswork. They're both valid, but presumably one's more popular than the other, so use that one.

99% of the time you should go with the most common reading. If the author wanted a rarer reading they would put it in furigana. As for words with various keigo readings, 明日 for example, it'll take some practice in order to recognize situations calling for the use of keigo.

When I asked that question, I was just given a 「文脈で判断するしか無い」 and given examples like 人事 じんじ　vs ひとごと or 生物　なまもの　vs せいぶつ and how they would be pretty easy to figure out with context. You just have to get used to it. Though, sometimes I'm still curious as to how things like 艶やか　あでやか　vs つややか are supposed to be discerned. I guess you'll have to hope that the author was kind enough to provide furigana.