Rotating an object 90 degrees doesn't work all the time. It goes all crazy on me then I end up deleting it and trying again. Moving only works sometimes. It either moves the entire object or clips a part off then you can move that and scale it. Likewise scaling only works sometimes also without having a clipped object. And i noticed if you do something (I forgot what it was) it can bug out and your guy falls through the platform.
Lol. In all seriousness... Lane is correct. But also... many things can "bug" out and cause you to go through colliders. And in near every case - its the user settings and controls (code too) causing it. As for rotate move scale.. not sure what reference your talking about. The rotate tool . For eg. Can be used by pressing and holding CTRL and gettin precise incremental rotation
Usually I use the gizmos in the scene view to make coarse adjustments in position, rotation, and scale. Once I'm close I switch the the appropriate fields in the inspector to fine-tune. It might be just me, but I like nice round numbers and try to reduce the number of decimal places if possible. I admit the rotation gizmo is hard to use. Also keep in mind that you can click and drag on the field labels in the inspector to make coarse adjustments and I often use this method too. The editor has a lot of magic that goes unused, IMO. Be careful of nesting scaled objects, it can get weird.
Check that your game objects position has been reset to 0,0,0... also make sure that any gameobjects are not offset. it sounds to me like your are using a model that's like a .mb format.. are you using ..FBX? I noticed that I have had some WIERD issues with rotating and moving a model (it moves, but then the geoemetry gets warped/distorted) when I import an asset as a .mb instead of a .obj or .fbx file... so it is probably some issue in the modeler's exporter options