It's funny, I thought that would be a quick google search away, but I wasn't able to find anything about that either. Unfortunately my Gotek is setup on a Compaq Portable 1 and I can't use anything other than 360k floppies with it anyway, so I can't test it out either. I would expect that it should "just work", but can't tell you for sure.
However, besides just trying it out or if anyone else knows, a couple of other things that might help you:
Dual drive support with a single Gotek (very much a WIP, but looks like it's partially done): https://kivijakola.fi/projektit/2023/02/26/gotek-flashdisk-dual-drive-support/
Making a DOS image from Linux: https://askubuntu.com/questions/484308/create-floppy-images - my thought here is that you could make a dos 1.44mb image, mount it and a smaller 360k or whatever image, and then copy the contents to the larger 1.44mb image. You should be able to do something similar in Windows with software such as PowerISO etc.
Finally, if nobody else has a solution before then please update us when you try it out, this would be great to know.