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so here is the situation, as in your small test, before a tempo map node is added:

and this is after a tempo-map node of "120 2/4" is added at bar 2, as in your example:

as you can see, the marker "Mark" stays at bar number 3, despite the time-signature has changed (from 4/4 to 2/4, which doesn't affect the time of the MIDI events already laid out); if the tempo was to be changed (as show below, from 120 to 90bpm) the marker stays at its original bar number (bar 3, while the bar location and the MIDI events gets moved accordingly to the tempo change):

sorry to tell, this is quite intentional: tempo, time-sig and marker nodes are anchored to bars (numbers), always as ever was. :)

can this explain the OP issue?

br.