I think it's best to build the site for search engines. We are actually discussing this approach at my company right now. Rather than just telling our clients that we are going to build them a pretty web site, we are also pushing the importance of structuring the site to be easily read by the search engines. Especially our e-commerce clients where their business thrives from the search engines.
I work closely with the production staff to ensure that they are including Title tags and ALT tags, building the linking structure in a way that allows the search engines to navigate our clients sites. We do encounter head-butting a lot b/c the designers want to do what looks best, but myself and the other web marketers want to have our clients sites built for the search engines.
I guess understanding the firms approach to building a search engine friendly site is what your concern should be. Also asking for references or results of other clients. A couple of our clients end up having us build the site, but then go to a seperate firm to completely optimize the site.
http://www.oneupweb.com/ really puts it into perspective:
Optimization Firms - team of professionals working on your project, great customer service, annual programs range from $30,000 - $100,000
One Man Band - single person within a web company with enough knowledge about the industry, usually find one tactic that works and sticks with it, Annually packages range from $1,000 - $20,000 and usually come in cookie cutter A, B, C packages
(OneUpWeb suggests to ask specific questions about their tactics and then follow up by doing a little research on your own to be safe.)
Software Systems - companies tried to automate the process of
SEO, popular among entrepreneurs and small business managers, usually people with little or no knowledge of
SEO purchase the software, has a couple drawbacks, but is pretty affordable to the budget conscious businessman
Hope this info helps.