@Alex Protsenko - My thoughts based upon my understanding of what you have shared...

Projects

As you have noted, you cannot add non/-team members/Guests to Projects – this is noted in the FAQ section of the Projects help center article:

Can I share projects with people outside my team?
- No, but you can share particular boards with people outside your team. Check out possible options here.

With Guest access, your only option is to add the Guest at the board level.

Create a Team per Guest

Depending on the number of Guests you have, rather than a Project for each Guest, you could create a separate team for each Guest (something only possible in the Consultant/new Business/Enterprise Plan).

While you still have to move all the boards to the new team and add the Guest to each board, an added benefit should you decide to add the Guest as a paid member for a period of time is that all of the boards are already in a team/workspace that you could then easily add the guest/new team member to that specific team.

Our issue is that the Miro links are on a Learning Management System, and we cannot paste individual links for each user, only a general link.

Only option I can see her is an intermediate step of adding any of the guests board links to another system, e.g., a document or spreadsheet in Google Drive or OneDrive, and pasting that one link in the LMS.

… or instead of a Google/OneDrive document, you could of course use one Miro board with links to other Miro boards :)

Thanks @Robert Johnson 
This all makes sense, in the end will be difficult to automate, but we’ve altered the way we’ll use Miro in order to make it work.

Thanks for the advice!