I would be comparing file and folder counts at this point. I’m sure there’s some way to automate the comparison of entire directory structures and file sizes, but I’m not familiar with any such tools on macOS. I use WinMerge in Windows, so perhaps you can find an alternative to that.
I have seen large discrepancies between file sizes on different filesystems, and it can vary wildly depending on the size of each filesystem block and how many files you have (a larger number of smaller files can have a greater difference between actual total size and total disk space used for example because of wasted block space).
Having said that I would still want to be sure, so it’s worth the exercise of figuring out exactly what is different. Like I said before, even if you traverse manually and find one difference (one file shows a different size on Nextcloud and Dropbox) that will probably give you a big clue.