In all MEP designs, especially those of Pipes the invert level is the inner bottom of the pipe, please make revit MEP tools understand and respect invert level both when creating pipes as well as when annotating invert levels.
The current workawround is to manually calculate the center of the pipe minus the radius of the pipe then when inserting a pipe always deduct or add it to the actual invert of revit, because Revit treats the center of the pipe as the creating line.
Then another workaround to annotate these is to use the spot elevation tool and make it see/read the bottom which is not the true bottom cause there is a thickness to the walls of the pipe.