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Some slicers have the ability to output verbose gcode i.e. gcode that has some comments in it such as layer numbers etc...

My question is, will the overtasked poor arduino have any difficulties in processing commented gcode vs uncommented gcode?

Most hosts remove the comments before they send it to the Arduino, so it's largely irrelevant.
There used to be issues with some host/firmware combos, if the comments were sent to the firmware it would cause issues, but as far as I know most of the current firmwares ignore badly formed gcode lines now.

I was intending on manually modifying some aspects of the g code and uploading that to the printer and prefer that the code has atleast layers indicated as comment.

So uploading that gcode would not cause a major issue.