Only if you feel that it is. Whichever plane youre most comfortable in ..fly that exclusively for the final polishing flights but if its minor stuff, a switch here instead of there then shouldn't be a problem. If its the actual six standard instruments in a different layout then I might be a bit concerned. I'm not sure Ive experienced that (hence why its standard) though I'm sure its possible.

Regardless of changes in the location/layout you should be and most likely are repeating a sequence even if its not apparent. I missed how far you are into it but instrument flying is rarely haphazard and I doubt your instructor is either. Of course some element of muscle memory is built into following a procedure but the majority of it is a mental exercise IMHO.