Hi thunderbird,
Welcome to the Mattress Forum! 
Latex Mattress Factory is a member of this site which means that I think very highly of them and that I believe that they compete well with the best in the industry in terms of their quality, value, service, knowledge, and transparency. They are extremely knowledgeable about latex and different configurations, and I would not hesitate to recommend them for your consideration.
[quote]Our initial plan was:
6" 38 ILD core
3" 38 ILD topper
9" cotton cover
But now I’m wondering if there’s any noticeable difference to go with:
3 x 3" 38 ILD toppers
9" cotton cover
It seems like both would give us 9" of 38 ILD latex, but the second option is actually $171 cheaper in the Cal King. Is there something I’m missing?
[/quote]
This is a question that pops up once in a while, so it gives me the opportunity to post about this again.
There would be little if any practical difference between two 3" support layers and a single 6" support layer if they were all the same type and blend of latex (which they are in your case – 100% NR Dunlop) and the same ILD and were inside a tight fitting cover. Two 3" layers would respond a little more independently and because the elasticity of the top 3" wouldn’t be connected and “pulling back” on the bottom 3" when it compresses and “in theory” it may act a little bit softer but in practical and real life terms most people wouldn’t notice any difference in terms of performance or firmness. If a single 6" core with a third 3" comfort layer was a good match for you in terms of PPP then there would be little benefit in having multiple 3" layers that were the equivalent ILD.
Also in “theory only” … two 3" layers that were exactly the same ILD as a single 6" layer could be less durable over the course of a long lifetime because they will act more independently and abrade each other slightly but I don’t think that any difference would be significant or even measurable in “real life” terms and the other factors that affect durability (see post #4 here) such as the firmness of the layers would play a much bigger role. It certainly wouldn’t be a concern of mine.
On the other side, multiple layers would have more options for fine tuning though both before and after a purchase. The main advantage of having more layers in other words is that for those who need it can provide more options to customize the layer combinations either before a purchase or by rearranging or exchanging layers after a purchase. While this is attractive to some people … it can also add some complexity that may not be necessary.
Outside of a mattress with more layers having more options to customize the mattress, if a mattress is a good match for you, then one isn’t inherently any better than the other.
If you’re thinking of staying with all latex, you are considering one of the better values available. You certainly could make a DIY all foam mattress out of firmer HR polyfoam, but this would be less durable (while less costly) and the comfort would be different as well.
If you’re considering the cotton stretch-knit cover on the Latex Mattress Factory site, that would be one of the more affordable covers available.
While I don’t continually monitor the pricing of the members of the site or elsewhere, many of the site members (see post #21 here) offer component covers. I also have various component suppliers broken out individually in the component post here.
I’m looking forward to learning about what you decide to do.
Phoenix