I've never purchased flat scales for my Mules but I think the difference would be obvious in your hand by just holding a Mule w/o any scales or it or w/some paracord tied around it. I personally do not like the feel of the knife like this.
The contoured handles fit nicely and comfortably in my hand and, given the choice, I'd never consider buying anything else for them, even though the flat scales are cheaper.
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Something to also consider is that the Spyderco Mule Bolatron sheath is specifically designed to fit a contoured scale.
I cannot insert and fully seat a Mule w/o any scales on it into the Spyderco sheath and the result would probably be the same w/flat scales on. So, if you buy flat scales for your Mule, you'll probably have to use Spyderco's (or another) leather sheath to carry it instead.
There are sellers on EB and elsewhere who make flat scales for the Mule and corresponding kydex sheaths to use them with.
So, you could buy flat scales from Halpern and Mule sheaths designed for flat scales from these other vendors which "should fit" provided the Halpern scales are the same thickness as the scales made by these other vendors.
None of this mattters, if you buy the Halpern contoured scales to use w/the Spyderco Bolatron and/or leather sheath.