CIS 2020

Just in case, let me remind you that the tournament regulations were changed (after participants had already started registering).

The tournament rules were added on March 10th. A couple of days later, the list of templates was changed. Before this, there were no rules, and after this, the rules haven't been changed. The clause about qualifying matches was added specifically on March 10th. Players who submitted applications without the rules implicitly agree to participate regardless of the format.

So, what prevents (or prevented) holding online qualifiers, as it was done in the very first CIS tournaments?

Well, with such a situation, it is difficult to predict anything; until the last moment, it is unknown who will be able to come and who won't. You yourself understand that the time frame does not allow for conducting a tournament with an unlimited number of participants.
The idea of regional selections (even if online) is very cool, in my opinion, but it is difficult to implement in the current realities and requires serious development.