Sounds like a decent plan, be sure to remember that you need to convert the save files from mister's format to a raw format regular emulators use if you want to transfer them to the flash cart.Re-Completed the gen 2 pokedex, about to start gen 3. I don't have a flashcart yet so I'm going to start by playing on my MiSTer FPGA and then later transfer my save over to a real flashcart.
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I could probably play on an emulator but I like the filters for GBA games that the MiSTer has
I use https://savefileconverter.com/#/mister for that, and it works quite well. If you've never used it beforehand the previous link has most of the settings already correctly selected, you'll just have to pick the correct platform (obviously GBA here) and it'll spit out the correct format. For the other way around you just select the other arrow so it changes the conversion direction.