It isn’t a problem, it is how the software is designed. Of course it will increase and decrease the size of the clip if you adjust it on the timeline. You are telling FCP “take this in and out, which was 3 seconds, and slow it to 50%, thus making it 6 seconds. Or, take this 3 second clip, speed it up 200% and make it 1sec 15 frames.” You are saying use these ins and outs but adjust the speed.
Best solution is option 1, load the clip into the viewer, mark IN and OUT, hit APPLE-J aned adjust the speed, drop into the timeline.