The official encoder pack installs to foobar2000\encoders; amending installer.ini with
PreserveDirectory3=App\foobar2000\encoders
would make user installed encoders persist fb2kPortable upgrades.
Also, foobar2000\components are foobar2000 shipped component dlls, that are rebuilt with every release and should probably not be preserved; user components as of v2.x reside in profile\user-components{,-x64}.
Finally, as more of a feature request, could fb2kPortable online installer include both 32-bit and 64-bit versions, like ccPortable for example? User components are architecture-specific, not sure about the config in general.
On the next release, encoders will be preserved and components will not. I had mistakenly thought user components would be added to components in the portable config but that's not the case.
As for 32-bit vs 64-bit, the vast majority of foobar2000 components are 32-bit only and will not work on the 64-bit version. So, having both in it and automatically choosing 64-bit for most users (since most users are running 64-bit Windows) would mean most component wouldn't work for most users. I run foobar2000 32-bit locally for just that reason as none of the components I use are available as 64-bit. So going 32-bit only was a purposeful choice.
Sometimes, the impossible can become possible, if you're awesome!