In such cases (or any others too), do conductors highly customise the full score?
Conductors do not typically produce the score. This is done by the publisher, or, for a new work, the composer or a professional copyist. As noted in the other answer, the conductor typically makes notes in the score, but it's not usually possible to modify the grouping of multiple instruments on one staff, for example.
Older works may be available in multiple different editions in which editors have made different choices about how to present the piece. For such works a conductor may choose a particular edition based perhaps on choices such as that. But even so, most editions will follow the practice reflected in the composer's manuscript. Generally, composers and editors all follow standard conventions, and deviating from them would not generally have a lot of benefit.
In the present day, with computerized music notation, it is somewhat easier for a conductor to produce a customized full score or even a complete set of performance materials. But it is still a huge job, and most conductors won't be likely to do it. Furthermore, for works protected by copyright, the conductor would need permission to do so, which might be denied.
it may be easier for the conductor to transpose or change the meter of some parts.
This is tantamount to sacrilege in classical music (except for renaissance and earlier music, as note values have been inflated over the centuries and there have been other significant changes in rhythmic and metrical notation). But if a conductor wanted to do this, it would be necessary not only to change the score but also to change all the performing parts. Otherwise it would be too confusing to try to communicate with the orchestra during rehearsals, because the conductor would have to remember to translate from the meter in the full score to the meter in the players' parts.