I don't think this is as big of a problem as you do.
Regardless of the instrument's origin (bought for big $ from company or open source built), scientists are going to run positive controls. It's a common practice for GOOD experiments. In this case, apply treatment X to a mouse, and you should see response Y as measured by the instrument. If you don't see response Y in the positive control, you cannot trust experimental results. If the positive control give expected results, then reviewers have little choice but to accept the experimental result.
You need to do the same thing for fancypants commercial instruments to make certain they are working properly, operated properly, and the rest of the experimental variables (the mice, the treatment) are as expected.
Bottom line is that if the homebrew instruments work reliably for the positive controls, they will be easily accepted.