I’ve never seen either of those behaviors. Can you share an example SKP file in which those things happen? We can try it for ourselves and see if we can reproduce it.
I copied and pasted part of the geometry into the attached SKP file to illustrate what is happening.
In attached file when I use the Trim tool to trim the siding at the window trim it will delete the wide board on the lower window. If I thicken the trim board so the back of the siding and back of the trim are not in the same plane it will trim properly.
If I trim the siding at the right of the window and then proceed to try trimming the same piece of siding at the left side of the window it shifts the right piece of siding over 1" for some reason.
In my copied SKP file I have not been able to re-produce the copying of the trim piece trimmed to a different area of my drawing like I do in my large model drawing.
I can reproduce the first thing you describe, too. I’m not sure if it’s a normal thing because of some of the intersections. Probably not. At least as a work around you could temporarily make the trim thicker with Push/Pull and then take the thickness off after the trimming is complete.
Another work around that seems to work is drawing a temporary extruded rectangle the size of the overall window with trim to trim siding to and then delete when completed.