I can confirm that the option to reproject is not present in SS2 PowerGeopak. It does show in PowerGeopak SS3. I assume before you were running MIcrostation SS3 with Geopak SS2. PowerGeopak SS2 runs with Microstation SS2. It is possible that the reprojecting option was added to SS3 and was not part of Microstation SS2. I would need confirmation from one of the Geospacial guys.
In PowerGeopak SS2, you can use the Data Acquisition method that you are familiar with.
In PowerGeopak SS3, Data Acquisiton has been replaced with OpenRoads technology.
In SS3, you should do steps 1 and 2 the same, but, for step 3, go to Terrain Model > Import Terrain Model from Point Cloud
That tool offers the option to filter (as shown in the capture below).
Then, you could export it to file (if you wish)
