Hey Dave... i'm glad you brought up the SEO point.  It is a common misconception that by using a subdomain based on a third party URL that it will only helps that primary URL.  In fact, by the very nature of what IDXbroker provides, it primarily works to the advantage of the individual agent's/broker's website.  In this case, the subdomain you listed above alternativerealtor.idxco.com, not only redirects to your own home page (http://www.alternativerealtor.com), but it also extends your potential SEO across all search engines online by creating a plethora of additional indexable content that is driven right back to YOUR website.

Let's take a look at an example.  I searched for the term "Eugene's Alternative Realtors RMLS" in Google.  I got the following results (http://www.google.com/search?hl=en&safe=off&rlz=1B3GGGL_enUS230US231&q=Eugene%27s+Alternative+Realtors+RMLS&btnG=Search)  Keep in mind that Google does display different results based on IP location and search history, but overall the results should be similar across most access points.

When performing this search above, the very first result is a link back to your site that is based on the subdomain you mention above (alternativerealtor.idxco.com). As you mentioned, this is not your URL, rather, a URL (subdomain) that is registered to your account as a subscriber of the IDXbroker service.  When you click the link that is indexed in the 1st position in Google (http://alternativerealtor.idxco.com/idx/2401/featured.php) it takes you directly to the Alternative Realtor's featured listings page.  This only helps you as the Realtor, because now you have generated traffic to your website that is relevant to your business.  This doesn't send traffic to IDXbroker, and is not some spammy technique to pump up the page rank for that domain either.  This is done by design to not only give you the ability to integrate your HTML and CSS into your IDX driven pages, but to also increase your overall reach online that will go directly to your website.

The point here is that because you are using a custom integrated IDX solution (not a framed solution) you are able to actually get wider SEO and search engine coverage as a result of using this method.  In does nothing to hurt your primary domain and it only increases your overall exposure for your business online.  Anytime you can drive traffic directly to your website, it's a good thing.

Here's another example, try this search "Eugene's Alternative Realtors Listings" (http://www.google.com/search?hl=en&safe=off&rlz=1B3GGGL_enUS230US231&q=Eugene%27s+Alternative+Realtors+listings&btnG=Search) what I see is the top three search results all pointing to your website, the third link being the subdomain mentioned above.  Without the subdomain pointing to your website, this would have less of an impact for your brand name and you would actually have less overall reach across the search engines that drive traffic to your website.

Additionally, by using a targeted subdomain that points directly to your own website, you are able to further leverage a larger domain's page rank for your own individual benefit.  You mention that the subdomain only benefits IDXbroker, this in some ways is true, it helps drive the importance of all those that utilize that subdomain.  Think community of users here.  Because the root domain is idxco.com and not alternativerealtor.com this does help the overall ranking of that primary root URL.  This primary domain is now pointing targeted traffic directly to your website, because of this shared community and higher page rank.  So... the concern about this benefiting the primary domain exclusively is actually a bit of a misconception, as it is of greater benefit to each of the individual subscribers utilizing the global system since they all benefit from the increased ranking.  Meaning, as the primary URL gains in page rank and "importance" with the search engines, your segment on that domain begins to float to the top of the search engines because you are now a part of that larger network.

Dave...thanks for letting me rant a bit on this issue, just figured I would offer my two cents here.  I love to discuss SEO strategies (as you can probably tell) as i have been involved in this segment of the industry for a while now :)

Thanks!