Regarding having a field for Company which is a list of Users, I think it depends on how many users will be assigned to that company. Bubble documentation says that shorter lists in list fields are OK, but longer lists can slow performance (I think Bubble says keep it under 100, but check the documentation). I think the reason for that is because a long list embedded in a thing makes the thing data-heavy, which bogs things down, as discussed here: Alternative approach to the Bubble’s recent tutorials for list of things
I personally would only link it one way – having the User have a Company field. That allows maximum scalability and keeps the database efficient. Bubble should be pretty fast pulling a list of Users for a Company, since that search is done server side.
That said, with Bubble, the “right” database structure largely depends on how you are planning to search and show the data. There could be scenarios that would call for you to do the links both ways. For example, if the list of users for a company were minimal, and you wanted to show RGs of lots of companies and lists of users displayed next to each company, then #1 may be faster.