Hi @tom,
See these topics and their replies for some more useful information on this topic:
- Does MRtrix have water compartment modeling similar to NODDI?
- SS3T (or 2S3T) CSD Implementation
- Fixel-Based Analysis on single shell data
Don’t hesitate to click all the links to other posts and sources in these discussions as well, they’ll lead you further down the multi-tissue rabbit hole. 
As @rsmith suggested, another recommended read would be the original multi-tissue CSD paper; to get an understanding in how we generally model the signal in a multi-tissue CSF framework.
Performing just single-shell single-tissue CSD will indeed leave you with the “caveat” of overestimating the WM compartment, because basically all signal will end up in that WM (FOD) compartment. So anything that still generates signal at b=3000, which includes grey matter, and potentially some other types of (non-axon) cells as well, will end up in your FOD, leading not only to overestimation of the “apparent fibre density”, but also distortion of your FOD by spurious peaks and other noisy structures, further limiting your abilities for tractography or even separating fibre density contributions in specific fixels.
Hope this all makes some sense… if not, definitely go clicking and reading some stuff.
Cheers,
Thijs