Hello @Fridrik - welcome to the Community!
In answer to your question, I believe it is possible to create companies with the same domain but what you will want to make sure you do is disable automated contact association.
Contacts and companies are associated based on a shared domain, so this will get tricky if you have multiple companies with the same domain. Check out how this process works and how you can disable it here.
I’d reccommend testing adding two companies with the same domain, before doing any mass import.
I’d also reccommend checking out the parent/child company feature. In HubSpot’s CRM, you have the ability to associate two companies in a parent-child relationship. To add a parent or child company to an existing company record in the CRM check out this knowledge article.
I hope the above is of help to you, let me know how you get on with your test!