I just synced a 1000 pages PDF of 44Mb sucessfully from W10 (2.0.8) to Android (2.0.1) via a NextCloud server using E2EE. My Fairphone 3+ took over 5 minutes decrypting it, but hey, once the job is done its's done: it just works!
Repeated the process with a 149Mb PDF file and it seems the 100Mb limit has been removed, because it synced too without issues or advisories. This file took almost 20 minutes to decrypt, as expected, and now opens perfectly from within the Joplin app. Very happy with this! 
The files occupy 75Mb and 258Mb respectively on the server though, almost double their original size. is this due to the encryption?