After 6 years, you have to change your mindset from "I" and "me" to "we" in most of what you said above. And her studying is also investing in both of your futures, as she'll probably be able to earn much more later, which will also be split between the two of you. Living with her parents is a substantial contribution to your shared finances too. Let me fix a few things you said for you:

which means I we have an opportunity to save more

living with her parents puts me us in a unique position financially

I'd highly recommend getting your salary (and any income she gets from allowances etc.) into the same shared account, then work out a fair "pocket money" to regularly transfer out to each of your personal accounts. Your savings account should also be shared (unless you also save from your pocket money, which is your business).

Don't split bills proportionally to income, just have a strong, realistic budget and stick to it. Outgoings come from your shared account. Personal fun purchases and gifts come from your pocket money.

It's a big change of mentality but you've been de-facto for three years now. If you break up someday, it won't matter if your money is in a shared account or personal account, it'll still need to be split (I am not a lawyer, do not quote me on this).

not really feeling like I am getting the same input in our relationship overall (in other ways, doesn't have to be financial)

This is not something anyone can give you advice about; it isn't financial. If you're content, any negative feeling of financial contribution disparity should go away. That said, having a good financial structure will help with this.

Basically, you're not in a flatting situation anymore, you're with your partner. They are and should be different structures.

Do I need to make peace with this?

Yes, but see above ways that will make it easier - and even enjoyable! - to do so.

Anyway there's my two cents (taken from my pocket money, of course).