I think you are confusing the justification of the Physical and the Analytical models. How you decide to handle this really depends on what you are trying to do with your analytical model.
If I read your question correctly, you want the location of the top of the Physical beam to be at the level, while the analytical model of the beams and columns only goes to the bottom of the beams.
In that case, the correct justification for the physical model of the beam is “top”. If you want the Analytical model of the beam to be in a different location, you must adjust the justification of the Analytical model, not the Physical model.
To do this select the beam (or beams) whose analytical model you would like to adjust. In the Properties Palette, just below the Type Selector, there is a dropdown. Click on that (it should say “Structural Framing”) and choose “Analytical Beams”. This allows you to modify the analytical model for the selected beams.
Scroll to the bottom of the Properties Panel, and you will find the Analytical Alignment properties. Change the Start and End Alignment methods from “Auto-Detect” to “Projection” Then change the Start and End Z-Direction to “Bottom of Element”. This will change the projection of the Analytical Model of the beams to the bottom of the beam.
Note that this is the best way to do this in the absence of a structural floor element with an analytical model. Without the floor Analytical Model there, the columns will continue to auto-detect to the top of the physical column geometry. You would then need to adjust the analytical model of the columns to a particular offset in a similar way, or you could manually edit the column analytical model joins.
There are a couple other ways you could do this, depending on what your final goal with your analytical model. If the entire floor (Beams, columns, slab) is really constrained to some offset from the “Level”, you could simply add another level at a different offset and host all your beams and floor to that level. With the Analytical Model set to "Auto-Detect" you will get the host level instead, with the beams' physical model bottom justified.
You could also create a floor with an analytical model at the desired elevation (Floor Analytical Models have similar justification options). Set the floor Analytical Model to the appropriate location, and the beams and columns, if set to Auto-detect, will adjust to that level. (Note that this is only if they are within the Vertical Auto-detect tolerance, set in the Structural Settings dialog: Ribbon>”Manage” Tab>”Structural Settings” dialog>”Analytical Model Settings” Tab>”Tolerances” section)
Hopefully this gives you a better understanding of how the Analytical model works in Revit.
Joe
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