Your option and the buyer's option is to complain to itch about this feature. And you should. If enough people complain about this, maybe they finally fix this. It does not solve anything and only creates problems.
It seems to have been meant for one and only one situation: someone wants to pay for some content and ALREADY knows he wants to pay that bit extra to get the bonus content.
Individually priced files are botched completely. For one, they are not as it says on the tin, indvidually priced. And most importantly you cannot increase your payment. You will buy the same project a second time, instead of increasing your donation level.
Most devs use this feature to have a free game and a paid game on one project page - instead of having a paid game with a free portion on one project page. For the most part this works the same. But it majorly screws up bundles, discounts, price changes and whatnot. And it gets ridiculous if there is more than one tier.
Or in your case, a paid game with an extra tier.
Add the individual file as an extra project as a dlc and not as a bonus file with higher tier. There will only be strife and anguish. No one understands this pricing scheme, not players, not developers and apparantly not itch, as they should fix this already, otherwise.