What's the frame size? I have v-brakes with DiaCompe 287-V levers, so no travel agent for me. My rear rack is the Burley Moose Rack (the one that goes with the Piccolo trailercycle), but the chainstay struts are basically in the same position as they would be on the Tubus.
My Co-Motion tandem is a 23"/18" frame, and my Trek 520 is a 25" frame, so I litterally have seen both ends of the issue.
Here are a few solutions I'm thinking of. You might need to combine a few of them:
1. Open the brake arms wider (especially the left one) and change the order of washers accordingly. That way, the top of the v-brake will be further out and the Travel Agent should clear the left strut more easily.
2. Bolt the struts inside the braze-ons. I can't do it on the 18" Co-Motion, but there is plenty of space between the stays to do that on the 25" Trek 520. That way, the left (and right) struts clear the brake arms more easily. In theory, there is a very slight loss of stability, but unless you overload it with 80 kg, I doubt it would be a problem.
3. Re-shape the left strut to curve it a bit, or make it longer and attach it to the right side. It wouldn't be worst than old rack designs with only 2 legs and a single strut. In fact, it would be almost as good as the "approved" method.
4. Use a P-clamp higher on the chainstay and attach the strut there. Not as nice as the "approved" method, but still nicer than the Old Mountain Man rack, I think.