Second ? first-
Tag all not tagged looks only at if the object is tagged, not if it is tagged by a particular tag... so, no, there is not way to tag 2 all not tagged (unfortunately).
Now the first ?-
Tags work in section just like they do in plan... to tag bottom elevation, you would create/modify a tag (if there isn't one OOTB) to use the 'Bottom Elevation' parameter. Works just fine.
Martin Schmid
Product Line Manager
Mechanical Detailing and Electrical Design
Architecture, Engineering, and Construction
Autodesk, Inc.