It really should be that easy. Just fired up X3 Producer x64 and tried it myself.
I opened a MIDI project,
In one of the tracks I set the dropdown to "Clips" (I often have it set to "Notes"),
I click on one clip, it goes grey.
I hold Ctrl and click on the one next to it, both are now grey.
I right-click over the first one and the menu pops up (it did NOT pop up when my cursor was over the NOW line)
...and I select "Bounce to Clip(s)".
They are now one clip.
This does not work for you?