Different installation media types and registry conflicts

Hi, I've been using an installation of PortableApps, which is located on an External USB3 Hard Drive. This installation is a 'working installation', which I use to download and evaluate individual apps, with the intention of eventually placing a select subset of apps on a USB Flash Drive.

I also use this External USB3 Drive installation to run apps which I may use only occasionally, and thus prevent unnecessarily clogging up my Windows registry with local application installations.

A while back, I was encountering issues with programs that had been both installed locally on my hard drive (full installation), and also installed as a PortableApp on my External USB3 Hard Drive (i.e., VLC Media Player). These problems involved applications not being able to store their preferences.

After scouring the Windows registry, I discovered that programs installed as PortableApps on my External USB Hard Drive, were also registering themselves in the Windows Registry, thus causing conflicts with their (non-portable) counterparts installed locally on my hard drive.

I also noticed that a PortableApps installation which I'd made directly onto a USB Flash Drive did not conflict in this way, as its registry entries appeared to exist in a separate 'USB section' in the Windows Registry.

Assuming my observations are correct, my question is twofold:

1. Is there any way to run a PortableApps installation on an External USB Hard Drive without it conflicting with Registry entries from 'like applications' installed fully on the local hard drive ?

2. If I install PortableApps onto an SD Card and run it from my computer's SD Card Slot, will it behave (correctly) like a PortableApps installation on a USB Flash Drive, or (incorrectly) like an installation on an External USB Hard Drive ?

Thanks,
phay