Multiple MongoDB instances on same server

The reason Mongo/10Gen recommends against running multiple instances of Mongo on the same system has to do with resource availability assumptions. The mongod process assumes it's the only major tenant of the system, and running two such side-by-side will lead to overall worse performance than just running one mongod just with two databases.

Mongo is quite capable of running multiple databases under a single mongod process. These are discrete databases, just under a single master process. Each database handles its own authentication, which gives you separation. You'd run multiple mongod processes if you need different mongo versions for your products.

I'm not enough of an RDBMS DBA to know the best-practice arguments behind separating products by discrete database-binary processes, so I can't refute/assuage/talk-down each point. But as I understand it, accepted practice in Mongo environments is to have a separate database per product.