Stripper usually leaves a layer of dark smut that can be cleaned off by various acids. Caswell sells desmutt that works very well to remove it, it usually only takes a short time and the parts come out sparkling clean.
The bad thing about mechanically removing some of the anodize is if you do some of the part that way, and then use stripper, the stripper will attack the bare spots while it is still working on the anodized spots. Once stripper removes the anodizing, it starts eating the bare aluminum at a higher rate. It may or may not matter but it is good to know that in case it will matter on your parts.
There are kinds of stripper that remove anodizing and are virtually safe to the aluminum, but they are hazardous and not even used much commercially anymore.
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