I would not expect passthrough to look particularly good, nor even work, on a lot of PC monitors. Modern PC monitors are not really made to handle interlaced images.
Second, if you reset settings, then it will always revert to bob-deinterlace, because that is the default in the firmware. If you want to save the passthrough setting, save a profile.
Third, unless your display has advanced aspect ratio controls & zoom options, your only option (bar a secondary scaler) to correct aspect/positioning issues is to change H.Samplerate and adjust H.Backporch as needed. However, in the first case that can sometime lead to other artefacts, such as vertical banding/blurring.