You probably could, just add some shortening or oil to thin it down when you melt them.
I've done it both ways and really like how the chips taste. Biggest problem I found was that the once melted, then the dipped item can develop 'bloom' - graying of the choco when the temp changes because you have not tempered the choco.
As for Apti's comment I usually leave a small area uncovered so they are not touching the choco .
The candy melts would be better in my experience. Chocolate chips have additives in them so that they stay soft after being heated. That gets quite messy after you dip things with it especially if you live in a warmer climate. The chocolate on the pretzel tends to stick to the packaging it's in or to each other if you don't package them individually.
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