I wouldn't recommend MD3 due to its precision problems and lack of large size support. Use ASE instead for this purpose.
It's also possible to do it with an autoclipped model, but that would lead to many many thin clipbrushes which bspc (bot .aas compiler) will not like very much as there's an excess of hollow area to process. Sock's modified BSPC seems to work better for this
I think
this q3map2 fork is intended to work with "model maps" better though I never tried it myself.
I should mention I have a modelh/map hybrid level in progress I haven't worked on in awhile. The mountains/cave are models and they really raise the compiling time despite how low poly they really are.