While the Magnetospeed does affect POI and accuracy, separating accuracy and chronograph testing isn't that big a deal compared to the PITA it sounds like your confronted with.
Some people also make stands for the MS, keeping them off the muzzle. Dirtfarmer did one for his, and is very pleased with the results. You might ask him about it.
For the price, the MS Sporter solves a lot of problems for many handloaders.
My long tailgate bench helps. May be hard to use this concept on a short bench. Need room forward of the muzzle.
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