A few tips to ease your suffering
First -I feel your pain - There’s an extension called Archtiect Tools has a function to Flatten geometry or Move Geometry to “Z” which I use a lot to overcome the issues you describe. Edge Tools has a function to detect and remove stray edges nad close gaps. Cleanup3 can simplify geomtery.
A nice SU feature would be a set of options that allows us to decide if we want to lock geometry to a plane, or to allow faces to close around stray edges.
Second- Get used to using shortcut keys for the eraser then you dont have to right-click. i agree the Eraser is too quick to delete entire components. Maybe it needs to be tuned so that when erasing raw geometry you have to unclick and reclick to tell it to start erasing other stuff as well.
Thirdly, I find the same - some components are badly created with silly basepoints. If SU staff are not able to automatically recalculate base origins in all 3dw components then all we can do to overcome this is import them into a fresh SU model , check them, then copy &paste into our original model. I find the time it takes to do this is worthwhile because the compoents that cause the problems are usually amateurish and have multiple issues that I dont want loaded into my professional working model. Also, if you aren’t already, start using the website version of the 3d warehouse because the 3d Warehouse Browser in Sketchup is pathetic.
Good luck.