1. I don't understand advantages of using one over the other. It looks like ISB native gives me a few more buttons I can program (M-keys) and one less program using memory (Logitech s/w.) Am I missing something?
Generally speaking it is a matter of preference. The best advantage is that you can configure the device via ISBoxer instead of through the Logitech program (using memory isn't hardly an issue). This gives you the ability to set up G13-G1 to broadcast something to some other window, something that you can't do through the Logitech software. To do the same thing via the Logitech software, you have to assign some random key combination to be pressed when you press G13-G1, and then back in ISBoxer you then configure that key combo to send something to your other window. By using ISBoxer's native support, you cut out an entire step of the process! (And keep those extra key combos free)

I currently use the G-13, with mouse buttons bound to 'ctrl, alt, shift' so, each key on the G-13 can be mapped to 4 different actions. i.e. G4 unmodded can do action 1, ctrl + G4 = action 2, alt + G4 action 3, etc.

2. will ISBoxer native allow me to do the above mouse/G13 combos?
Are your mouse buttons bound to modifiers in your mouse's programming software, or in ISBoxer? If configured in the mouse programming software, then yes it will work exactly the same. If configured in ISBoxer, then instead of having your buttons send modifiers, you would instead want to bind your mouse buttons to change states in ISBoxer (e.g. toggle on a Key Map for "Ctrl" without actually pressing it and turn off the un-modified Key Map, opening up a set of modified Hotkeys)

3. Additionally, I would like to do a similar binding so a mouse button and the G13 stick, can either move a) everyone b) slaves only c) tank (or focused window) only. Is this possible as well?
Yes