This is true. Neither the article nor the CEO of the microwave drill company say why.
At that depth, rock isn't a solid. It behaves plastically. The traditional tri-cone bit used could make progress, but it kind of just started "massaging" the rock. The bit (as all bits do) wore out. They pulled the drill string out of the hole to put a new bit on. The borehole would close back in during the multiple days it took to pull 40kft of drill string out, change the bit, and put it back in. Progress was not possible.
Unless the microwave drill includes some enormous cooling system (that works 40kft down hole even when the drillstring is removed!), they will face the same issues.
Also, separately, I saw pictures of the resulting lab-drilled hole on LinkedIn the other day. The hole shows a high rugosity (qualitative description of the roughness of a borehole wall). Similar photo here - https://spectrum.ieee.org/media-library/image-of-a-rock-surf.... That's a ugly hole, and would be very difficult to run casing into it.
Further - traditional well drillers' #1 focus is controlling pressure downhole (typically done by varying the density of the drilling mud). If the pressure becomes too great, a blowout can happen, which is bad news for everyone involved (see the BP Deepwater Horizon incident). For geothermal wells, they presumably will try to avoid hydrocarbons. However, rock far above water boiling point can cause a BLEVE (boiling liquid expanding vapor explosion), which is also undesirable. Super curious to see how they intend to control bottomhole pressure with statements like this - "Instead of pumping fluid and turning a drill, we’ll be burning and vaporizing rock and extracting gas, which is much easier to pump than mud."