If you call Start-DscConfiguration and push a new mof file out to a computer, then yes, you’ll be overwriting what’s there (even if nothing in the mof has changed) and more or less resetting DSC’s timers. As long as nothing in the MOF has changed, then this isn’t really a big deal; your resources will just run their Test commands, everything will say it’s already configured, and it’s done.
The same is essentialy true for the DSC pull server; if the MOF file’s checksum changes, then the client will download and apply the new one just the same as if it had been pushed with Start-DscConfiguration. This will happen every time you recompile your MOF file, since it includes the date and time that it was generated (which will in turn modify the checksum.)
I only see this as being a problem if you’ve set your LCM to run in either ApplyAndMonitor or ApplyOnly mode. In that case, when you push down the new MOF file, DSC would wind up trying to correct any configuration drift again, instead of just reporting (or doing nothing.) If you’re set to ApplyAndAutoCorrect mode, then you won’t really notice the difference anyway, other than timing.