The allowance seems to relate to changes of rules with regard to self isolation on return to the UK. Portugal was never on the exempt list so the only change at this stage would be to put it on rather than take it off.

There is also the separate issue of FCO advice. Currently this is for all but essential travel to Portugal, but Madeira and the Azores are exempt. I can understand your concern that ABE could be extended to cover Madeira too, but it seems the BAH allowance doesn't relate to changes in FCO advice unfortunately, so any such change wouldn't seem to be relevant.

To note another obvious point, if your booking starts in JER it does not originate in the UK and therefore does not seem within scope of the allowance anyway. I understand rather than having exempt countries like the UK, JER just tests everyone on arrival.