It sounds like you are suggesting that we build our own custom circuit boards. The people that I work for do not manufacture our own circuit boards. We largely do not have the expertise to manufacture our own circuit boards. We are not electrical engineers.
The Advanced Photon Source has electrical engineers, but we are not part of the Advanced Photon Source. If we go to the Advanced Photon Source and ask them to build boards for us, they would probably quote a price and ask us if we have the budget to pay for that. Or they might say that they are too busy to do it for us. That would be especially likely now since the Advanced Photon Source is in the middle of a major upgrade.
In the end, it is better for us to find vendors that make data acquisition equipment compatible with 5 volt logic and buy stuff from them. That is probably true for most of the organizations that make use of the Advanced Photon Source.
I mean, you have to connect the MCU to your thing somehow, that's building a circuit, so you just insert the level shifty thingy between. But I have no clue about your seemingly highly specialized use case (which, why arduino of all things), so presumably you know better.
The Advanced Photon Source has electrical engineers, but we are not part of the Advanced Photon Source. If we go to the Advanced Photon Source and ask them to build boards for us, they would probably quote a price and ask us if we have the budget to pay for that. Or they might say that they are too busy to do it for us. That would be especially likely now since the Advanced Photon Source is in the middle of a major upgrade.
In the end, it is better for us to find vendors that make data acquisition equipment compatible with 5 volt logic and buy stuff from them. That is probably true for most of the organizations that make use of the Advanced Photon Source.