Is it possible to pay transaction fees from a different source?

Yes.

The token sender is determined based on the first transaction input, while other arbitrary inputs can be added to a transaction.

This allows to craft transactions, which use an input to tag the token source, but other inputs to pay for transaction fees. The token sender likely has a tiny fraction of bitcoins anyway, because he or she received the tokens in the past.

Unfortunately there is no built-in command for this, but it is possible to use the raw transaction API of Omni Core to craft such a transaction manually. As general guide, see the following tutorial:

• Use the raw transaction API to create a Simple Send transaction

In the next version of Omni Core, two new RPCs will be added to ease this process, which can be tested, when building from source:

• https://github.com/OmniLayer/omnicore/pull/658