I don't know if anyone has really answered your question. I see a lot of opinion but nobody has said unequivocally, CMS_Brand_X does "something" which is bad/good for SEO because of "something else" that can be backed up with facts.
My take on organic SEO is that to get the basics right, you need to do a few things:
1) Put together keyword rich document titles. This is vitally important to getting good SEO results.
2) Load up pages quickly. According to Google, the speed with which you site loads has a minor influence on your rankings. Minor but influence all the same [link]. This is up to the themer to achieve. A good themer will know their way around the CMS and will build sites that output optimized lightweight pages that load quickly without a lot ot bloat.
3) Add Meta Description tags. Just as the title tag is important, it is important to provide Meta Description tags. Search engines like Google don't tell us how important these tags are but they still indicate that although Meta Keywords are useless, Meta Descriptions hold some weight.
4) XML-Sitemap. This gives search engine spiders a cheat-sheet for your site: http://en.wikipedia.org/wiki/Sitemaps
5) robots.txt. I use robots.txt to dissalow search crawlers from indexing areas such as calendars and file directories that would otherwise bog them down and prevent the indexing process from being completed: http://en.wikipedia.org/wiki/Robots.txt
To get beyond the basics you might need to hire an SEO specialist who will help you with the flow of information and rewrite the information so that it is synonymous with the search terms you are targetting but I'm pretty sure both systems can achieve these basics equally well as long as you know the system so it's really up to your personal preference of which CMS you prefer. Maybe someone can provide an SEO benefit of one over the other that can be backed up by facts but I can't think of one myself.