These questions were also submitted to the Service Desk which we also replied to.
Basically in answer to the IRM question regarding .htaccess, yes each IRM could have it's own .htaccess.
You would want to take this Knowledgebase Article into account..
http://Service.FutureQuest.net/kba432
As far as the SEO aspects that would be a question for those that specialize in SEO, which may be one of the most complicated and confused subjects regarding web sites.
Seems to me that for every question regarding SEO there is a minimum of two completely contradictory answers...
-Bob