In general it should certainly be possible to generate correct full score and instrumental parts from the same project without requiring you to use separate files.
Just yesterday, Hugo Bouma shared his experience that problems with divisi can cause him to have to use separate projects for score and parts, but this should only come into play with very challenging and complex situations.
And we certainly want to know what limitations exist that might cause you to need separate projects for score and parts, as it is absolutely our intention that we should find solutions for those limitations or problems.