Usually when I play otb chess my opponent will leave the book lines rather early and we will just "play chess." I am ok with this because I believe that with proper play I should have a better position than my opponent, unless we transpose to opening lines again. Is this always true? Is it possible to ignore the opening lines and still end up with a good position?

Yes, it's very possible, especially in OTB play. Whether or not playing "your own" moves is objectively the best plan depends entirely on those moves and even more so on how you follow them up. Because if you surprise your opponent be prepared for him to surprise you.

Also, the chances of a solid novelty, especially early on, is unlikely. The odds of playing a novelty at all, good or bad, just for its shock value, is also unlikely because it is a relatively common pratice at all but the highest levels of play. But I hasten to point out that just because a move is unpopular does not make it bad.

In amateur games, the first person to deviate from known opening theory is most likely making a mistake, so yes with proper play you should have at least an equal position depending on what colour you're playing (if you're playing white than you probably have an advantage).

In regards to ignoring opening lines and still having a good position....

No, I don't think it's possible to ignore opening theory and come out of the opening with an equal position, you will almost always be at a disadvantage. Not to mention you will know practically nothing about the middlegame positions you are in since you haven't studied them in any detail.