I might have thrown a bit of extra stuff into my question by referring to primary and secondary. My questions is really about whether it is different to leave the beer in a fermenter for a few weeks or bottles for a few weeks.
The argument made at NTexBrewer's link seems to make sense. I wonder if Palmer changed any of his recommendations in newer editions of How to Brew. I know he is no longer much of a proponent of using a secondary. The only thing that doesn't make sense to me is the part where he says having more yeast in the secondary fermenter vs. bottles is relevant, since proportionally the yeast-to-beer ratio should be the same (though it would be higher in a primary fermenter, but that's not his claim). Headspace does seem like it could be a factor, and the different chemical make-up post-priming could also affect yeast activity post-bottling (something I alluded to in my OP in less specifics than Palmer).
Seems like there are some differing opinions on this. I only have one fermenter currently, so secondary is not really an option. I've been fermenting for a week and a day now, and I'm kind of eager to brew a new batch. This is my second batch right now, and I'm out of my first batch (aside from a couple special-occasion bottles). I want to be able to have a constant supply to drink, without investing in another fermenter right away. So I was wondering if I could just rack to bottles in a week or so, rather than keeping them in the fermenter for 3-4 weeks and then bottling.
I have a bunch of Grolsch flip-top bottles, so I was also considering racking to them and adding priming sugar later. This is probably overly complicated unless I use priming tabs, and would introduce some unnecessary danger of infection, but it's a thought.