Because they are less common - that's about it. Some covet the Subaru badge, or prefer the looks of one over the other...... TBH you can only see it's a BRZ from the front or close enough to see the badges so whether it's worth it is down to the buyer.
When I ordered mine in 2016 the top spec BRZ (Auto) was cheaper than a top-spec GT86 and pretty much ended the same (but BRZ looked better in my view!!). Then in March 2017 an MY17 arrived .. win, win!
The reasons are not quite as quoted above. The main reason is simple and this happened when the EU regulation of 95g/KM across its fleet applied to car manufacturers. Toyota with a slew of hybrids has its emissions targets exceeded and they don't need to pay a penalty. Subaru on the other hand has to cough up to EU as it has no cars below 95 threshold. Makes sense?
Otherwise made in the same factory by Subaru themselves for Toyota with minor changes. Toyota currently still has a base version and a pro version. Subaru only has the equivalent of a pro and by the way has apple car play / android auto enabled HU while I believe Toyota does not. Buy it from Subaru, you can negotiate. Get it serviced by Toyota, if you wish to keep it close to home.