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Even if you get more client exposure and the firm pays market, is there still a "prestige" disadvantage to beginning your career at a small firm? I mean, if you develop your own book of business (specifically in IP prosecution and IP counseling) wouldn't you still be solid lateral material later in your career, even for some biglaw firms? Are there other disadvantages associated with starting at a small firm?

Associates at the small firm I worked at get calls from headhunters occasionally. It really, really depends on the firm though. This was a big law boutique, so while it was small it was still attracting major clients and high end work.

The smaller the firm, the more likely it is to be quite specialized, and that alone is likely to constrict your exit options. But it can be exceedingly hard to generalize on these points. Keep in mind that while a larger firm may have better exit options in the aggregate, it's going to depend on your practice area within the firm too.

Very few people on TLS will be able to give you an accurate response. I would suggest speaking with CDO and alums who work in small firms.