If you took the time to throughly learn an engine, would you spend so much time wrestling with it afterwards?

If I was working on this full time the investment of learning an engine thoroughly would be worth it, I imagine. Game dev is a hobby for me, though, and what motivates me is making fun games. If I stumble across a game idea that's really fun and worth releasing to a wider audience there's nothing stopping me from building a better version of the game by hand at that point.

yes! you wrestle with it because the starting boilerplate is thpically a do-once operation. if you stay working on one project for a few years, you will no longer know how to start the next project, and with modern software, starting a new project in two years from now will be nothing like starting one now