I don't see an issue, and I don't really see House Mercere having an issue with other magi doing vis trading 'under their noses'
From my understanding of the Order, House Mercere are the only ones who have a good idea both where all the various covenants are and are perfectly capable of getting their hands on large amounts of vis of all techniques and forms easily.
Secondly, House Mercere have a proven track record of secrecy. They let you register your vis sources with them, as well as details about how to get to your covenant, and in return they collect your messages, inform you of news and offer vis, books, items, etc. for trade. They do all this without revealing either your or your covenant's location to any passing random who asks.
For the security-conscious magus, House Mercere offers an easy means of engaging in trade with other covenants - both for books and vis - without revealing your actual location or details of how to breach your defenses to the other covenant in question. It also doesn't prohibit trade in vis using the Redcaps as carriers - if I want to send 20p of vim vis to that covenant over there, and then expect to get 20p of aquam vis back, I can send it via Redcap. The Redcap will guarantee safe and secure delivery of the vis - it is what they do.
Where House Mercere shines is when the covenants doing 'local scale' vis trade run out. When you want another 5 pawns of aquam vis and the others just don't have it, you turn to House Mercere and pay their rates.
I figure the House has no issue with this. There are more than enough magi who want specific vis and don't know anyone personally who can supply it. In many cases, trading 1t:1f works out fine for the magus in question - and in many covenants I can't imagine the 1t=2f rule applying internally.
Throw in the Mercere 'charity' and usage of vis for the benefit of the tribunal and order as a whole (as opposed to simply giving it as massive vis salaries to their board of directors), and I can't imagine the house caring any more than they do about House Tremere not making use of their vis trade services.
Of course, if the House's vis income drops below their expenditure, you can expect to see less charity. The political ramifications of that would mirror many modern political issues, combined with the fact that actions which reduce the amount of charity in the world could well be construed as greedy and sinful.