>> no hardware ever supported both PPC and Intel ISA
It did. Intel-based Macs (starting around 10.5, whenever the hardware was introduced) ran PPC software via Rosetta, which made it easy to ignore the conversion problem, since existing binaries ran just fine. Rosetta was discontinued in 10.7, which was where the trouble started.
>> XCode is basically a front-end to LLVM which hopefully will allow us to compile 32bit for the foreseeable future
That's basically what I'm alerting you to. The clang compiler will presumably compile 32-bit object code for pretty much forever, but Xcode may lose the ability to package such code. Further, after a certain point there may be no universal binaries in their current form, so you might not have that option for the foreseeable future.
The take-away (as I see it) is that if you want to preserve your current business model, then you are forced to preserve your development environment as well. That means preserving both a suitable Xcode version and a suitable macOS version, because you can't even assume Xcode 8 will run on future macOS versions.