Hi @dusjagr. There is a base without space for the Pi for Version 7.0.0-alpha2, but it does not seem to be linked anywhere from the build instructions. There is a download of all the files for the release where you can find it. All releases of the microscope are at https://build.openflexure.org/openflexure-microscope. The relevent zip file https://build.openflexure.org/openflexure-microscope/openflexure-microscope-v7.0.0-alpha2.zip is quite large as it contains everything, but in the models directory there is the file you need microscope_stand_no_pi.stl.
Alternatively there is a simple hack in the “Where are you (OFM location survey)” thread https://openflexure.discourse.group/t/where-are-you-ofm-location-survey/771/16. The first link in that post has a microscope standing simply on long M3 bolts in the mounting holes. That is a Version 6, but the same idea would work on V7.