The benefit with an ONT (or even DOCSIS dumb modem) managed by the ISP is that they can do fleet upgrades much quicker as they don't have to keep all old protocols running. For instance the GPON -> XGSPON upgrade that some ISPs are running right now (or DOCSIS 3 upgrade) really only works well if you can turn off the old protocol which requires swapping out all ONTs/DOCSIS modems.
If customers bring their own stuff then you're stuck with these things for much longer.
Calix for some reason makes it easy to clone some models.
I have a post on this: https://www.neelc.org/posts/clone-calix-ont/
Now I'm in NYC with Verizon Fios where I don't need a cloned ONT. Woo! The Verizon ONT is big and has a huge power brick, presumably because of RFoG alongside GPON.
JTAG is a much lower level protocol, typically used for hardware or low-level software debugging. Serial/UART gives you a command-line interface to the software that's running.
Using a JTAG interface is a lot more complicated. If you're interested in playing with it, check out OpenOCD.