Investigation for the observation made in post.
"CPU consumption on AT went up to the maximum of 38% (w3wp.exe) while the GenCheckinNotesUpdateWorkitem task was executing on the build machine."
Case 1 - 3 msbuild processes in separate window - running GenCheckinNotesUpdateWorkitem on same team project for the first time
Case 2 - 3 msbuild processes in separate window – running GenCheckinNotesUpdateWorkitem on same different project for the first time
There are no issues in running multiple instances of builds concurrently for the same AT.