German Alps or Austria's Grossglockner Road
 

I'll be taking a 2 day 1 night drive, from Bamberg to Alps to Munich.

I was thinking to go to Berchtesgaden to get my Alps experience.

However, if it's spectacular scenery I'm seeking, would I be better off driving all the way down to the Grossglockner road in Austria, or will I be able to get a similar experience from somewhere within Germany?

If the weather plays along, the scenery on the Grossglockner road is absolutely breathtaking.
You will not find anything like that on the German side of the Alps, if only for the reason that the mountains are still not very high.
OTOH, it takes appr. 1 1/2 hours from Berchtesgaden to the start of the Grossglockner alpine road near Fusch.
The tolled section itself takes one hour to drive - in the unrealistic case that you never stop to take photos or walk around or have something to eat.
The total drive time on that day would be five hours. Without any stops.
IF you decide to do it, you must try to get the local weather forecast the evening before. Otherwise the whole trip would be for nothing.

IMO there is simply not enough time to do the Großglockner Hochalpenstraße drive with only one overnight, coming from Bamberg and going to Munich (which is serious backtracking), and to actually enjoy it.