That's a very good question. I wonder if there's actually an answer to it in the volumes of Dr Who archives. If they had effectively 2 autonomous systems, both of which could independently drive the body, then maybe their beats could be wildly dissimilar... but if they were tied in any way, well, that could get weird for the internal organs.
There was a long running theme during David Tenant's era where they a four tap motif, something like tatata tap, which eventually turned out to be the sound of the two timelord hearts beating.