Just to be clear, we're talking about elder-onset AD here. There are SNPs associated with early-onset (APP, PSEN1, PSEN2) that are also involved with amyloid production - and it's not clear those are connected with gut issues.
I'd go on about the decision to use early onset as a 'model' of the disease and so chase what amyloid issues (IMO a red herring) - but I'd expect you're sick to death of that one :-)
I've been digging into the BBB of late. "Barrier" seems to vastly overstate how impermeable to insults it might make the CNS. It's a highly dynamic system - and I'd expect that gut issues could easily influence its performance - particularly for APOe homozygotes as that leaves the astrocytes on hair-trigger.