I’m not quite sure but is seems as though the boot (supplier example only) is held in place by the console upper panel and the gear shift knob i.e. remove the gear shift knob, remove the upper panel, slip the boot over the gear shift and into the console box, replace the upper panel and then replace the gear shift knob.
Here’s an image from the 1991 MR2 service manual where it shows the assembly of the console box. Hopefully it is the same for your year model.
If the console upper panel is broken, missing etc (not sure if you meant this) it is also known as the shift boot trim bezel but I can’t find any for your year model, only from 1990↑
(click on image to enlarge)