About excluding constrained atoms in the RMSD atom list in MTD

[SebastianWellig]

In the tutorials for MTD, it is mentioned that one should exclude all constrained atoms from the RMSD list (see Conformers of transition-states, for instance). However, in doing so, won't I loose some degrees of freedom that I actually want to bias, i.e. all bonds to these atoms, except the ones involved in the transition state, or even the angle between the three atoms involved in the transition state and so on?