Although the anodizing will shrink the holes, it is of little concern. If you reamed the holes according to the blueprint specs, then its not an issue, since it is the exact method used by all manufacturers. The actual pins are slightly undersized to accomodate the anodization growth.
As for being a manufacturer...a home builder is NOT considered a manufacturer, by BATFE definition. A home builder is a "MAKER" and does not require any type of Federal license (State Laws may Vary) and is not required to follow the laws established for manufacturers. The definition of a manufacturer can be found on the BATFE website, but basically, if you are in the BUSINESS of making firearms for sale, then you are a manufacturer. As for the subcontractor and stamping issues, they don't apply as you are not a manufacturer.
As for your specific question..yes, you can have it anodized at a local shop. They also are not considered Gunsmith's in the eyes of BATFE unless they are engaged in the business of finishing firearms. A local anodizing shop doing an occassional firearm wouldn't be considered as being 'in the business'.
As for being present, my guess is that you would have to be there while the work is being performed, as you would technically still be in control of your lower. I couldn't find anything specifically addressing this question in the ATFE FAQs.