Jack, inconsistencies will always be inconsistencies and thus undesirable. Particularly, if MuseScore produces them without the user's consent, it is a bug.

What you are talking about is differences between bar lengths and metric signatures, which may be due to mistakes, but also occur regularly such as anacruses. Some composers do not want any metric signature at all. In such cases, we have to tell our software what exactly we mean, particularly if the length of a bar differs between the staves of a score.