I haven't played Magic: The Gathering in over 20 years, so my interest in this material is strictly for what I can use elsewhere rather than using the CCG's setting. Therefore, I will continue to approach it from the angle of mining parts of it for a 5E Freeport campaign.
For my past columns about using D&D Fifth Edition sourcebooks with Freeport: The City of Adventure, see the Freeport 5E Index.
One obvious way of using Dominaria with Freeport is to place the City of Adventure within that world. I lack the necessary setting knowledge to identify the most suitable locations, but the Spice Islands or the fringes of the Voda Sea seem likely from the very brief overview in this document. (Perhaps one of the two Tolarian Academies is identical to the Wizards' Guild in Freeport?) The merfolk of the Serpent's Teeth would become one of the many Vodalian tribes, and their ties to that federation would give them greater influence (especially over shipping) than is assumed by most Freeport titles.
References to "The Continent" in Freeport sourcebooks should be read to mean Aerona, and in most cases would apply to Benalia specifically. Northern barbarians would hail from Keld, elves from the Llanowar forest, and orcs and goblins from the Ironclaw Mountains.
The Church of Serra provides good opposition to the many demonic and diabolic cults that operate in Freeport (which might include Belzenlok's Cabal), and would likely be the origin of most of the inquisitors and crusaders who have visited the city in the past. However, due to the city's history as a pirate haven, the Church is unlikely to achieve the lasting presence or popularity there that it holds in Benalia. In fact, in campaigns where the PCs are as amoral and corrupt as the city in which they operate, Serrans are far more likely to be enemies than allies.
The other approach to mixing these two settings is to take whatever bits and pieces you want from Dominaria and drop them into your preferred campaign world for running Freeport. For example, the aven previously appeared in Plane Shift: Amonkhet, and thus could be associated with the distant land of Hamunaptra. The three new monster stat blocks (homarids and two species of kavu) are suitable for nearly any setting, but fit Freeport especially well, and the tables of quests, sites, and villains are easily mined for inspiration for any campaign.