1.) This is really tricky from your brief description. Hire a lawyer asap if you're even remotely serious about leaving and doing your side hustle full time. Not trying to discourage you, but there are going to be some IP issues to sort through that shouldn't be ignored.
2.) Ideally if you leave and apply to YC, you want to have your boss say positive things about you. It's not just for YC: every single investor will ask you about the jobs you've had before you started your company. If there are any red flags that you or your company are going to get sued, they won't invest. The best way to handle this is by ending on good terms (and ideally getting some sort of IP release agreement with the help of a lawyer [but that may not be feasible, given the new direction your current employer]).
A) have no specific ideas/ideals built into the software from your current company B) do not leverage company resources, assets or even insights to have improved the capability of your product (i.e. your knowledge is complementary, not created or originated close to the product the company has created) C) Prove that you deployed your product capability prior to having shifted and/or joined the company
1) In the end, if you really are big on this -- you should probably leave the company and be able to demonstrate to yourself and your investors that you deployed capability (or planned product) prior to joining the company.
2) I would be less concerned here assuming your time here is under 6 months, you can simply not choose to display it (i.e. the idea that you'll be YC ready in the next 6 months -- enough time for you to belittle/reduce/erase the time you were at the current company -- would mean that you're a lot further along. Thus by the time you're YC ready, none of this will have mattered.
P.S. I think you'll be good with YC. As a member of an existing top accelerator (Forbes B2B top rated) in Silicon Valley, most of them do not care if you have a similar idea (speak to the impact and traction instead of the idea), I believe your differentiation (not having taken from the company) and purity of code (not having been influenced or using company resources) will set you free.
There are a lot of different ways to game out a situation like this and they depend a lot on your relationship with your boss, what outcome you want, and the specifics of your agreements.
If you feel your own chances are somehow better than hers, then explain the situation, and try to part on the best possible terms. Definitely talk to a lawyer now if this is a likely course. You may not own what you think you own.
Otherwise use what you have to your advantage at the current company. Maybe folding your work into your employers is worth additional equity or salary.
Worst case scenario, you find the we-own-everything-you-produce-period clause, in which case what you did in the complimentary industry on your own time is still the property of the company.
So yes, I agree with the advice to consult a lawyer and bring all relevant legalese for their review.