I noticed in the manual it says that a PC must either be placed in the VGA or HDMI/DVI #2 Input rather than just an HDMI Input (both look identical, as you know)
OK, you've read the manual, that's a good start...so what happens when you connect your MBP up to input #2?
And what happens when you go VGA?
First, I was wondering what the difference between the "HDMI #1 and #3" inputs and the "HDMI/DVI #2" input is? Would plugging the PC into the HDMI/DVI #2 input allow it to be full-screen?
I have no idea, I've never owned a plasma let alone your model; I'm a DLP and LCD guy because they're much easier to hook up to computers.
Second, the only way I'm able to get it full-screen 720p via HDMI #3, is to set the Samsung to Screen Fit mode (rather than the 16x9 mode I have for my other HDMI inputs). Will this Screen Fit mode harm my TV given that Pixel Shift is disabled?
Plasmas, sometimes, can be tricky to set up as computer monitors into the HDMI port, especially since they're not actually 720p, as in 1280 x 720, but rather 1024 x 768.
So, reassess why you're plugged into #3 when the manual says to use #2 for a PC.
It's not uncommon for a TV, internally, to process/scale different inputs differently, i.e. to have one HDMI input that's "special" and others that are not. It may be that you can only get a certain max resolution in one of them and not the others, you won't really know until you tap into a knowledge base for that particular set and learn its intricacies. There's probably a big thread on this display in the AVS flat panel forum, find it, read up on how successful other users have been hooking up computers to it, and what they had to do.
But my guess is, you'll keep coming back to that native resolution of 1024 x 768--what I'd do in the meantime is read the whole owners thread and test both going into VGA and into HDMI #2. Maybe one of them will allow your Mac to fit the screen exactly, and wouldn't that be nice (because tweaking with SwitchResX to fill out that last inch or so can often be a frustrating experience.) If you're lucky, you'll find other Mac users who have already done the legwork for you and have determined whether it's less of a hassle to go VGA than into HDMI.