I guess the terminology is important to define if one wants to have correct specifications. Otherwise, one could mix the requirements.
Frame structure: Are you referring to the baseplate?
Foundation of machine: Are you referring to the concrete foundation? With/without grouting?
Skid: Are you referring to the driver and driven equipment?
Structure to mound machine: more than a meaning
" I have read a text about foundation machine design that mentioned to avoiding resonance we should consider operating frequency and blade pass frequency but don't mentioned about separation Margin for them"
You are right, resonance must be avoided but not necessarily by defining the separation margin. Some references call for maximum vibration on the foundation. Some call for weight ratio.
Anyways, see if the below print screen form again API 610 if it could help a little.
Regards- Ali M. Al-Shurafa