Wouldn't it be faster to just kill her ?

When you kill Muffet, there is an extremely lengthy unskippable cutscene where a smaller spider scrolls on screen, back off, and then gets a flower and does it again. It's like 20~ seconds. Since you need to abort Genocide at some point in Core, and because the spider donut instantly spares Muffet without the cutscene, doing this is the fastest way to progress.

The other thing is with Neutral Glitchless you have to abort Genocide run eventually. You have to spare a boss somewhere, and Muffet is the last possible boss you can spare to abort. If you kill Muffet I believe you are stuck on Genocide.

You are not stuck until you kill all 40 mosters in core, as you can still fail to exhaust the kill count and fight Metatton without killing all monsters, which would lead to a failed genocide run.

Oh right, I didn't though about the cutscene. Thanks !