There isn't an editable file to prevent these errors, but you can easily fix them post footprint creation.
First off, I would make sure you are entering the inputs right. I say this because for chip capacitors/resistors/inductors, it asks for the MAXIMUM height, not the minimum.
These generated a correct looking STEP body for me, but if you'd rather just keep the pads and draw the body yourself, here's what you can do. After generating the footprint, click the step body and delete it.
Then first select the layer that you want to draw it in, usually something like Mechanical13.
Click Place -> 3D Body. Select Extruded, type in an overall height (1mm shown here). You can give a standoff height too if desired, this has no effect on shorts detection / DRC. Click OK.
Draw a rectangle where the part should be. IPC wizard will have left behind a prior shape you can follow (we deleted the 3D body already though). Right click to close the polygon. Hit Esc. Switch to 3D view and see the body as drawn. You can double click it to change the color/capacity/etc. or modify settings that were in the initial dialogue box (like change the height).
For your second issue, regarding the SOD123FL footprint, this one is even easier. After generating the footprint, just draw your own cathode designator using the silkscreen layer and the Place -> Line command.
Again, I tried this with the IPC Wizard just now and it created a cathode designator, so maybe your tool is a bit out of date.