It seems to me that it’s been hard for people to suggest what to do (apart from telling you what tools are available) because it’s hard to see exactly what you’re trying to achieve. I get the impression that you have different strands of music playing simultaneously at different tempi, and with some parts containing a MIDI recording of a natural performance, including naturally varying tempo, but that the recording was made ignoring the Cubase metronome - you can decide whether or not to let it stay unrelated to Cubase’s metronome.
Was your reason for considering the warp tool that you wanted to make the grid line up with your MIDI recording? - ie was it that you had a freely played recording and wanted to make the grid match the recording (ie to get Cubase’s bar lines in the right places)? If you do that when the original recording was played with a natural varying tempo, then, of course, Cubase’s tempo will be adjusted to reflect the varying tempo of the original performance, yielding a click of correspondingly varying speed.
If the original variation in tempo is what you want to continue hearing, any further musical tracks added in time with the original recording will have to follow the varying tempo of the original recording - whether or not you’ve made Cubase’s tempo align with the original recording. Alternatively, you can edit the tempo track however you want (after aligning Cubase’s grid with the performance) - eg to make the pulse regular, but then you’ll lose the natural timing of the original performance. Or, as said in an earlier post, you can temporarily switch off the tempo track to make the speed constant.
Cubase can only have one musical tempo at a time - though (probably using linear mode to prevent unwanted tempo changes), you can overlay tracks with their own constant or varying individual tempi, but, of course, no more than one of a set of diverse tempi can be reflected at one instant in Cubase’s tempo track.
FWIW, one option is to let freely recorded MIDI parts retain their natural tempi, unrelated to the Cubase tempo. You then have the option to alter the speed of all simultaneous parts by editing Cubase’s tempo track. Also, you can stretch or compress individual MIDI parts by using Logical Editor to alter the note lengths and timing, though that’s rather fiddly.