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> While I eventually ended up fixing the performance issues in my game, I can’t help but think of scenarios where problems could arise later that are unfixable due to limitations of the tools I’m using.

Only if you don't want to get your hands dirty with the layers you're using.

The trade-off with an abstraction layer is that every layer introduces bugs/decisions which may be a concern. But you can always (if it's open source) tweak the layer(s) below.

Moreover, why not finish the game and make your next project in something new.