Assuming they are sharing the same board package versions.... do you have the same board options selected in both IDE's?

Also in Microchip Studio do you have the vMicro > Debugger > Debug set to Off?

Thanks for confirming that the Serial Debugger was the issue here.

Any delays within the Serial Debugger can be removed by enabling the vMicro > Debugger > Full Speed (No Throttle) option.

If there is a lot of information within the trace and a lot of trace points firing quickly, it can overwhelm the PC Serial Port, but from your description this does not sound to be the case.

It is also best for time critical tracing to disable any of the Monitor Digital/Analog Pins to save this also being sent back every break/loop().

When working with Stepper Motors (which are often ms or us critical in pulsing) I have always found it best to complete a full "movement" without any debugging, and if you do want to see within such time critical elements then the video below helps to explain how the @Plot charts can be used with the Serial Debugger for this applciation:
YouTube: Visualize Millisecond Events from Your Arduino - https://www.youtube.com/watch?v=wwRawju55nk

The Atmel-ICE (or other Hardware Debugger) may be useable for your board, if you can confirm which board you have we can advise better.

The Hardware Debugging is generally slower than the Serial Debugger for these time critical purposes, as it has to constantly stream back far more information to the PC than the Serial Debugger.