I have joked in the past that ATC forget that aviation is 3D, but this sounds like it is true.
Does this mean that altitude is not normally used for separation, and aircraft at different altitudes will not be permitted to cross paths without horizontal separation?
Vertical separation is a key component of ATC's toolset.
Within a terminal area there may be altitude limits designed into certain SIDs & STARs that provide that vertical separation. Example: an aircraft departing on a SID being vertically separated from another arriving on a STAR where there is a crossover. There are other traffic management practices that may be involved as well.
A visit to an ATSC is worthwhile to understand how it all works, ATC practices and the constraints they work with.
ERSA GEN FPR section 5.7 was indeed added some years back to advise the minimum overflight altitude that is most likely to facilitate a clearance. Availability is of course always subject to traffic at the time of the request, and RWY use at ML is also a factor.
Before filing a flight plan for a CTR/TMA transit it would be worthwhile calling the relevant TMA Traffic Manager (phone numbers are in ERSA) to discuss your requirements, determine the appropriate route/tracking and the likelihood of clearance availability.
And as
PA39 has said, filing a flight plan instead of just calling up assists ATC.