Good news - I haven't exactly 'solved' this issue, but I've found a workaround.
In the pre-game editor, go to Nation -> (whichever nation you want to edit) -> Information and then amend the most recent season co-efficients. To reflect real life with Italy and Germany getting the extra spots at the expense of England, you will need to bring England's co-efficients down a touch (to around 20.000 but might need a bit of trial and error to find the right balance, you don't want them losing an extra spot) and bump Italy and Germany's co-efficients up by around the same amount.
This doesn't fix the root cause - the FMRTE custom start date can't replicate the unexpected real life Champions League results from this year that have impacted the co-efficients so much, so the game plays out with England gaining an extra spot. But it allows you reach the same end result by falsifying the co-efficients from previous seasons.
Full disclosure, I haven't had a chance to fully test this yet so I don't know if it will cause other problems further down the line, but I'll get to that soon and will update either way.