Do the required savings for this prerequisite (and credit) need to come only from building energy, or also process loads?

The energy savings are based on the whole building energy use—building and process. LEED does not stipulate exactly where they come from, but there is a greater burden of proof on the project team to demonstrate savings in process energy. As a default, process energy should be modeled the same in both baseline and design case.

Our process load is higher than 25%. Do we have to justify that?

It is common to have a 80%–90% process load in a manufacturing facility. The 25% default in LEED is based on office buildings. If you think your load is lower than 25%, it is recommended that you explain why in a short narrative. It is also recommended to briefly explain it if your load is 25% exactly, since that level commonly reveals that the process loads were not accurately represented.

Our project has a large process load—75%. Despite our efforts to make an efficient HVAC design, the cost savings are minimal. What can we do to earn this prerequisite and be eligible for LEED certification? Is there any flexibility in how we model the p

You must model accurately. Since you don't have enough savings in the building energy, find savings in the process. Either you will be able to demonstrate that compared to a conventional baseline the process being installed into the factory is demonstrably better than "similar newly constructed facilities," allowing you to claim some savings, or the owner needs to install some energy-saving measures into the process to get the project the rest of the way there. Either option can be difficult, but not impossible.

Is it acceptable to model a split-type AC with inverter technology compressor as a heat pump, like modeling VRF?

Ideally if the software you are using cannot model a technology directly then seek a published workaround related to your software. If you can't find a published workaround then model it as you think it should be modeled and explain how you have modeled it in the preliminary LEED submission.