Spacing Issues when removing Cleffs

Select the note and in Inspector use the chord offset, not the element offset.

Unfortunately, I think you're looking at this backwards. The per-staff scaling setting only happens to produce an approximation of the correct result in this case, but it comes with all sorts of issues, precisely because it is not exactly what you are looking for. The only time you should ever use the per-staff scaling value instead of the global scaling value for the score is to have one staff different from the others in your score. This presupposes you have multiple staves, of course, and that at least one of those staves is at the global scaling value for the score (eg, the per-staff scaling of at least one staff should be at 100%).

If there is no other staff at the global scaling value (no staff with 100% per-staff scaling), it throws off the layout caluclationss, which depend on the per-staff scaling being relative to the sizes of the other staves. And actually, even if there are other staves are at the global scaling (100% per-staff scaling), there are known bugs if you try to use values greater than 100%, because in fact this facility was never intended for making one staff larger than others - only smaller. So, there end up being a number of calculations don't take the possibility of the per-staff scaling being larger than 100% into consideration, thus leading to bugs that are not detected in tests, because again, this wasn't what the facility was designed for or normally used for.

So again, unless you want one staff different from the others in your score, don't use per-staff scaling. Always use the global scaling for the score, found in Layout / Page Settings. Elsewhere you referred to this as the "MSN method", but that's a misnomer. It's the correct method for scaling scores in general for almost all use cases. It just happens that MSN is one of those use cases and was used as an example in a link earlier. But it's not for MSN primarily. It's for all scores, to set the overall scaling for all staves. Then you use per-staff scaling only to deliberately produce effects where one staff is different than the rest.

Also, BTW, a reason not to settle for working around the bugs in per-staff scaling >100% using manual adjustments is that those adjustments will then break your score if/when the bugs get fixed. or if the layout of the score gets changed for any reason - changes to the spacing algorithm in future versions, or you end up changing where you system breaks are, or you add key signatures, or change the rhythms, etc.