I had a similar issue where it linked my brother in laws gt to my ea account we couldn't play madden and other ea games together because of it, we contacted them last fall and they wouldn't do anything. I was looking at my ea account for something else a few weeks ago and found a setting where you could remove a gt and it gave you a warning that you could lose account data related to fifa and apex, it didn't work though so I contacted support and it took all of five minutes for them to remove his gt from mine, and we didn't even lose any data.
I'd rather not risk losing my Twitch Prime loot. I don't doubt I would lose them, seeing as they aren't listed anywhere on my account that I could find.
Some time back I made a bunch of long posts in these Xbox threads about my experience with the EA account system. When I finally got a One X I found out that my EA account on the Xbox side was different than the one I used on PC and PS4. It was created back during the 360 days and was tied to an e-mail account that I no longer had access to. I couldn't pass any of their verification checks to prove I was the owner of the EA account. After a ridiculous amount of going around in circles with EA support I was finally able to get a support tech that sent me a code to my Xbox Live account to prove that I owned the EA account and then was able to change the e-mail address. I'm still stuck with 2 separate EA accounts, so I'll never be able to do any cross progression stuff across platforms. Also, separate Twitch rewards as you've mentioned. Their account system is garbage.
I do recall those posts, they reminded me of my original struggles at the time. I gave up caring to fix it awhile ago. Hell, I can't even play SWTOR anymore, one of the fans on my ancient video card started to fail, so I pulled it and have been using the integrated graphics on my CPU for a year or so now.