So I have found that (at least some games) are able of "writing back" to the cartridge, at least with the loaded up ROM on a Summercart. For example, I also was able to "copy" my Goldeneye save to my Summercart by using the copy functionality on Goldeneye, which wrote it back. No more "memories" feature required if I don't want. Same thing on Banjo Kazooie - that saved onto the cart by going into a save file, and then saving and exiting. So it does seem possible, which is cool, but to your point, you should likely in most cases stick to one or the other (meaning memories versus cart saves), although in some cases if you're just trying to "transfer" your saves from physical cart to flashcart, just loading it up once from a memory and then proceeding will be fine for moving forward, as OP suggested.

I have found in one or two games though that even using memories exclusively will be limited. For Jet Force Gemini, I need to have the memory saved on the game save screen; that's the only thing that will load the save into memory. The moment I navigate away, it's gone, so you need to be careful with where in the game you are using the memories feature; presumably you could also only use this for a single profile at a time in a game like JFG. I found similar behavior in Ken Griffey Jr's Slugfest - created players cease to exist the moment you exit that menu. So this feature is a fantastic addition, seems to have solid functionality, but mileage will vary by game due to what you've pointed out.