I would install the sprockets "on the marks" and then when you reinstall the timing cover and balancer, CHECK TDC.

Use a positive stop:



Put in no1, making sure the engine is NOT on TDC, and there is room for the tool to go in.

Gently wrench the engine around until it stops "on the stop" and make a temporary mark on the wheel right under TDC on the tab

Do the same CCW

True TDC will now be halfway between these two temporary marks, and if the original mark was correct, that is where it will be

You may just be seeing the difference caused by chain stretch

As someone else said, when the marks are "dot to dot" the engine is ACTUALLY on "no6 ready to fire", not no1. If you do not rotate the engine you want the rotor pointing to 6, not 1.

You probably did not pull the dist, so it should be OK except a minor movement to retime (for chain stretch)