I know someone that has a specialized molecular CLS license and did it at SJC. The problem with it is that it limits you to reference labs and those that only do molecular work. Basically Quest and LabCorp. This person worked at Focus but now they are closing and are moving to SJC. Your options are limited and your pay will be. Reference labs do not pay as well as hospitals.
Your job will basically just be PCR as that's what molecular is. Now molecular is getting pretty popular and is the next wave of the future. However, hospitals don't do molecular, they ship them out to reference labs. Even a generalist CLS can do molecular.
Now a specialist micro CLS is more valuable. You can work in reference lab or hospitals because all hospital labs have micro depts.
I do think the generalist CLS is the best option though. You can work in any department and can move up to supervisor, manager, or director in a hospital or reference lab. If you just get molecular, the most you could be is a molecular supervisor, but I doubt you could be manager of a whole lab.