Hi Turtlebed,
You can see my thoughts about individually encased layers in post #2 here.
I believe you probably mean http://www.organicmattressshop.com/ which is their site for the mattresses they make that are sold through other retailers but doesn’t include all the information or products that are included in their main site.
I don’t think this is something I would worry about with any reputable manufacturer if the latex hasn’t been sitting in direct sunlight and was only being stored in an appropriate environment prior to it being sold or used in a mattress.
Mattress factories where foam is cut are dusty places and would certainly not be as “clean” as a typical mattress showroom and this would be fairly normal as well.
You can see some comments about Mountaintop Foam in post #6 here and in post #2 here and there is more about the different types and blends of latex in post #6 here. It is also available at Spindle Mattress which is one of the members here who sells 100% natural latex made by Mountaintop foam at very good prices and has a layer exchange policy. Bedinabox also uses it in their latex mattress here as well. NOTE ADDED: Nest Bedding is also now a member of this site
A DIY mattress can certainly be a challenging and frustrating project (see the comments in option 3 in post #15 here and the posts it links to) but it can also be rewarding. The best approach to a DIY mattress is a “spirit of adventure” where what you learn and the satisfaction that comes from the process itself is more important than any cost savings you may realize (which may or may not happen). It’s one of those things that some people are very happy to take on and others may choose to avoid the time, complexity, research, and frustration that can be part of the DIY process.
Like everything else the “value” of a mattress purchase depends on all the criteria and parts of “value” that are unique to each person.
Phoenix