An example, I think, may prove helpful.
I am the sysadmin for a single college that supports approximately 20 departments comprising 225 distinct web domains. Rolling out certificates for each of these supported sites would certainly be doable under the current ruleset - if a little time consuming initially.
The wrinkle begins. Each of our departments have their own evolving ecosystem of servers and network technologies which do not always fall under our direct support umbrella. In this case, it gets a bit more complicated. If a faculty member installs certificates for a number of machines in her lab which burns through our allowance - thats inconvenient, but still probably not a deal breaker since that admittedly does not happen every day (or week, in this case).
The winkle wrinkles more. Additionally we have 12 sister colleges/schools which are also comprised of their own departments, sub-units, and research areas. If one of these units decides to create certificates for a battery of course WordPress blogs, our ability to potentially have access to the 20 certificates gets a bit dicier.
The wrinkle wrinkles wrinklier. Not only are there 13 primary academic units, but you also must consider administrative divisions which cover everything from financial administration to athletics programs to student support services. Many of these areas will have evolving marketing campaigns, academic initiatives, and so on which will have web systems requiring certificates.
In short, if even a small, itsy, teeny number of the sysadmins in this population decide to tinker with LetsEncrypt on an ongoing basis, there is a virtually zero percent chance that any specific unit or area can have reliable access to certificate generation. Lets not even start thinking about the impact that students - working on computer science projects, for example, will inevitably have on the quota.
Not saying all of this to be contrary, for the record. I certainly understand the reasons for the limits and the rationale behind making sure this service is not abused. Our assertion is simply that it would be wonderful to see High Ed be taken into account in a specialized way - given the unique nature of our support ecosystem.