Time synchronous averaging - MATLAB
The answer to your question "is it a problem" is really up to you to determine. Sometimes the simple things work well enough.

There is a technique called Dynamic Time Warping:

https://en.wikipedia.org/wiki/Dynamic_time_warping

and Matlab has a function dtw

https://www.mathworks.com/help/signal/ref/dtw.html

which can use to figure out if it is a problem.

I suggest you pick a reference interval, that would be the closest to the average shaft interval and use that to warp the rest against.