I have been unable to contribute in the past due to not meeting the reputation threshold and couldn't even respond to comments in my own question. This has really turned me off of Stack Exchange, but I think you would benefit from waiving those requirements for people signing up using .edu emails or using email domains from whitelisted companies. Just coming from one of those organizations proves enough they are real accounts and can vet them.
You should be able to comment on your question (and also answers to your question), and if you can't that means you need to merge your accounts.
You should also be able to answer most questions (which is different from commenting), with the exception of protected questions. If you encounter a protected question you should answer other questions instead to get the 10 rep required to answer it (or do anything else that gets you rep).
Although it's not as big a threat as a disposable email, there is still potential for people with .edu emails to spam and troll. I'm pretty sure that some .edu addresses go to elementary, middle, and high school kids. I even know some college kids who like to shitpost.
And the commenting restrictions are not just to prevent spam and trolling. They also prevent people from using comments before they know what the site is about and posting bad comments (e.g. "me too", "thanks", "pls send me the answer"). These comments can be a nuisance for anyone who gets notified to them (mostly the OP) and need a moderator to remove.
Thus, I would not be open to letting low-rep users comment, no matter what email they have.
So basically... Eternal September all over again?
People only "really" have .edu accounts if they work in a school (and not necessarily as a lecturer) are in school,(which isn't always a reflection of intelligence) or are alumni in an institution cool enough to let them keep their accounts.
None of these reflect, on their own, the trust that they can use their powers for good, not evil.
Besides, as per the help center
Please note that you can always comment on your own posts, and any part of your questions. However, commenting on other people's posts is a privilege gained from earning reputation - if you haven't earned it yet, try to get comfortable writing answers first.
You should be able to comment on your own posts at any rep and need a 50 reputation on most sites comment on any other user's posts (meta's 5, but you can look up the equivalent on any site's help page)
There might be another problem - possibly the question is on another account (which happens), but your proposed solution in no way will solve the problem you're facing.
Also a bad idea because many non-US institutions don't use the
.edu top level. I'm unaware of any easy to access list of academic emails.