Let’s Encrypt is a trusted, established alternative, it could replace Microsoft for long-lived software certificates.

Uh, no it could not.

First of all, the whole point of signing software is to ensure it comes from a reputable source. Let’s Encrypt signs certificates with an automated process that does no verification whatsoever of the identity of the person asking for a certificate. It would make the whole process completely pointless.

Second, Let’s Encrypt has stated themselves over a decade ago that they have no intention of doing this because it would render the whole system pointless.