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What sort of configuration are you trying to accomplish? How do you want to setup your virtual domains? Generally speaking, as long as you control the domain you can add and use it in Office 365 as you'd like. In a way, our system is already using a virtual domain configuration.
We are using virtual domains in order to deliver email for a selected set of users to a different mail server.
My only concern is, can we relay on Virtual Domains to be supported in the foreseen future?
That depends on what you mean by virtual domains, as it really sounds like you're just describing domains and namespaces, instead of a virtual domain scenario. Can you give me a specific example of your configuration?
We are using office 365 with the default FOPE settings to 90% of our users/mailboxes. The MX is assigned to Office 365.
For the rest we need to deliver the email to an alternate email system(not exchange).
in order to do that we create a virtual domain in FOPE, preparing a CSV of the selected mailboxes/users, assign them to FOPE virtual domain and modify the virtual domain setting to relay the emails to the alternate system.
The question to be exact, is this option of creating customizable virtual domains in FOPE is a supported feature that will continue to be supported in the future or that is another way to redirect the emails as described?
There's no indication that Enterprise subscriptions will lose access to the Forefront Admin Center in the future. I'm not certain as to how much you can do with virtual domains in that space, but you may be able to configure your mailflow in such a way as you'll use connectors rather than virtual domains, as you would with these instructions: