Hi,
I'm using the Hybrid mode because we have both 32 and 64-bit versions of our 'server' software. The installer is complex, with a lot of custom dialogs and calls into our dlls for licensing. I'd rather the setup executable be larger than have to maintain two SB projects.
I'm pleased to report that after failing to reproduce in the sample, I discovered that the 64-bit keys already existed - the installer did not create them so they were not removed. You can consider issue (2) resolved.
I've attached the hybrid.sbp file to illustrate issue (1). Select '32-bit', and you'll notice the mode gets changed after including the VC++ 2013 32-bit runtime (the 64-bit version defends against this using the WAS_X64MODE variable).
Jon.