I would think that any essential PHP code in templates should be 'filtered' out by b2 in template editor, except the usual author/e-mail/comment tags. This saves a lot of potential damage to an edited file. When saving the template, b2 checks if the necessary code has been put in place; if not, it does just that but only if one or more author/e-mail/comment tags have been put in the file (to prevent any disasters from occuring should one be just editing a casual file).

Otherwise, it would also be wise to follow the Blogger way. b2 can process the filename (which is put as a preference) and accordingly format the tags. I think this is very much slower and harder to fix than the first one suggested.