Bomps (aka 'Pushy Rock with Eyes') have a hardcoded location in their object behaviour. This can be circumvented in SM64 ROM Manager via hex editing (see C5 in Lost Lunatic Trials). However, there is a simple workaround.
The effect of this hardcoding on the large Bomp is it overwrites the Z coord. This means that as long as you use Large Bomps along a single vertical plane like they appear in the vanilla game then you can simply rotate and move your level to that location in your modelling software and set the other coords as normal.