Hello Ciaran,
sorry for my late reply.
Its not at me to find something to be suitable
I think, according to J4 and the Child Template possibility it might be logical that the custom.css is in the media folder.
It could be helpful if the path is correct in the J4 templates in the custom css option tab. Means not templates/j51_xxx/css but the media/templates/site/j51_xxx/css and maybe a short note like: "Pls shift your custom.css file to the folder ... after a migration" or something like that.
IMHO it's not a big deal to shift the css file after the migration to the correct folder. And one can find the correct folder if its pointed out in the custom css option tab.
But on the other hand, I am not a "normal" user. We are a web agency, thats our daily work (and mostly woth your templates)

and currently we do a lot of migrations.....
Kind regards
Oliver