I had a special plate made, 3/16 inch thick, and shaped to fit below the left brace attachment point. However, this raised the brace too high, pushing it up against the hood. Also, the threads of the shock tower bolts did no longer extend all the way through the nuts. So I decided the plate was not a good idea. I replaced it later by a 1/16 inch plate, which did give me a bit of clearance.
Philip Airey explained that you can move the bypass actuator by releasing the two bolts holding the metal actuator bracket. The holes of the bracket are slotted. This allowed me to obtain a small amount of additional clearance between the actuator and the brace. Unfortunately, the engine rocks a lot compared to the car on acceleration and deceleration, so the actuator did still hit against the brace during driving. I tried varies angular orientations, but they do not seem to make a difference. (Philip's method does seem to work if you have the older metal actuator case, though).
Finally, I ground the strut bar down using dremel and file. Actually, I filed it down until the threads attaching the bar to the end bracket started showing through. But with all this, the brace still hits the actuator during driving. I think however that the impact may be weak enough to be acceptable. So I have adapted a wait and see attitude.
The Flying Miata brace spanning above the engine.
The clearance I obtained between brace and the top of the bypass
actuator, when the car is at rest. The white stuff on the actuator
is "Type-Out", which I used to see whether the strut bar still
hits the actuator. You can see the amount of the brace that I filed
away above the actuator.
Another point of view.
Here you can see the black stripe in the Type-Out made by
contact with the brace.