It's got to be something I did, I found the first iso I rolled with snapshot last night and burned it to a cd, this was before I started hardcore stripping, I had just removed Libre, Gimp, replaced the browser, and added a few programs.
Installed it and it worked exactly as it should, no issues with pkexec.
So somewhere between there and where i'm at now, there must have been some small library or app that seemed like it wasn't doing anything, and didn't show up in dependency/dependants lists as being connected to anything, that must have played a small part in connecting pkexec properly.
Sure seems though, that the default behavior if it didn't find that tidbit, would be to error out, NOT assume root privileges and go ahead and open the programs.
I may go back and try some more, but for now I took fsmithred's advice and made extra .desktop files for gparted and synaptic, used gksu and set the others to not display. Rolled a new one this morning and gonna burn it here shortly, install, and test.
Was trying to keep it as close to the default settings and behavior in Devuan as possible, but if they are working on putting out some livecd images it may be silly of me keep trying to go that route, though I still think there is a lot of merit in a minimal iso.
A wasp stung me on the butt today. I am literally butthurt.