Ok I managed to do it. You can use the "agreements" tab on a nation in FMRTE 2017 to add an agreement with the EU. Worked perfectly. I did have to buy the PC version but it only took a few minutes to do so you can just request a steam refund afterwards.
I like to play FM by taking a small team up through the English leagues, finding talented young EU players and developing them then selling at a profit. Hard brexit has made this impossible. Really poor design choice not letting us choose our brexit scenario IMO. I'm 4 seasons into my game so I...