I think, as a GM, my first response is that your Mercere has a lot of non-magical resources already developed. This probably took a lot of time to do, and once we also understand that time cannot be spent twice -- on both studying magic and developing mundane resources -- this suggests that the character is either a decade or so out of Gauntlet, or his magic is weak for his age, or both. I might suggest to the player that he consider focusing on one or the other: either a Mercere magus and Seeker for artifacts, vis, and lost lore, OR a mundane Mercere who is also a master merchant and shipping magnate with mercenaries. That sort of character would be a Companion character, and your "magus slot" would be open for something else.
But my sense is that the player would probably not want to do that, and would like to keep on plan for a magus who is deeply embedded in mundane affairs. One of the challenges is that the character you describe is Wealthy, and magi cannot take Wealth because they already have 4 "free seasons" and their wealth is tied to the prosperity of their covenant. If you are joining a game in which the covenant is already very rich, you may be able to simply handwave the shipping and mercenaries and so on, and say they have always been there but never became relevant to a story until now.
Alternately, your magus is coming from a former covenant, one which was fantastically rich and where he slowly acquired all this support over years. If you have the money to pay for a merchant fleet and mercenaries, and Gentle Gift to ensure they don't resent you, then you may not need additional Virtues to explain that. You can pick a Story Flaw to represent some of these mundane ties, but it would probably be a Minor one because it also gives you some benefit. More important that Virtues might be the Abilities necessary to manage this far-flung network, including languages (the languages spoken in the Middle East are many and varied), Area Lore, Profession: Merchant, Leadership, and Bargain. This is where the XP problem comes in, because Abilities get expensive at the level you need them, and those points can only be acquired by a combination of age and the opportunity cost of weaker Arts and spells.
Your magus might benefit from a factor or other mundane merchant who handles all this stuff for him. This would allow him to focus on magic, and leave the running of the merchant stuff to his consigliere. Then you could take the consigliere as a Minor Story Flaw. He helps you out, and is very useful to you, but like a Magical Animal Companion he also gets caught up in stories and you have to go rescue him or deal with the fallout.
The book you need is CITY & GUILD, and I presume you have TRUE LINEAGES, where House Mercere and its distinctive magic and house structure is detailed. C&G details the various ranks of Merchant, required Abilities, Virtues, and so on. There is a magus ship captain in THROUGH THE AEGIS, but he is Tytalus. It may be worth noting that -- with the exception of the template character in the core rulebook -- nowhere in the 40 books of AM5, among over a hundred magi with fully-developed game statistics, is there a magical Mercere. There are many reasons for this, both in-world and out-of-world, but it means that a magical Mercere is a common place for players to go, because "it's not been done." In fact, this is exactly what Christian Andersen is doing with Janus of Mercere, who will be of interest to you: https://forum.atlas-games.com/t/anulus-connectens-janus-of-mercere/10509/1