Whatever the clinic's preference, in many areas, you still have a choice of DME. The one our clinic referred us to would have ordered the wrong wheelchair, full stop. DMEs often recommend what they're getting the biggest incentive on that quarter. From what I have heard, I agree with Diane that Permobil tends to deliver faster. But the DME still has to come out [preferably to the home, not clinic, esp. if the home has unique features] and do the final fitting as it were. Sometimes tweaks need to be made a couple of times more in the first few weeks. Thus, proximity can be a consideration and it's preferable to be in the part of town/the county that it's not hard for the DME staff to get to [e.g. "Yeah, we usually get out here once a month" would be a bad sign], unless it is not a problem for you to go to them.
Some clinics are much more involved than others in specifying brands and models, so don't presume one way or the other who is more involved (the DME rep or OT/PT at clinic) until you know. Then negotiate with that person. At our clinic, the PT simply signed the order that was prepared in full by the DME rep. Your dad needs to be accurately measured and the chair specifier needs to know something of the house/yard/setting involved. So it's best to do the measurements at home and be able to point to aspects of the home -- driveway, thresholds, narrower doorways, acreage, old bathroom, garage, whatever, that the wheelchair will need to deal with. If you are going to use transit, you need to take note of the width/weight restrictions for bus and train ramps. If you live in a city and will be wheeling there, the chair must accommodate curb cuts.
You want the DME who's going to be efficient and accurate in submitting the claim and providing service, not the one who takes the clinic staff to lunch most often, so make a list of local DMEs in network before you talk to clinic. Unfortunately, there has been a lot of consolidation, so choices are more limited than they used to be, but you should know what they are if any.
To make sure there are no errors or omissions, you should review the spreadsheet listing all the attributes of the chair before the DME submits it. Some DMEs, for example, will omit the seat elevator because they think the payor will deny it and they're worried about collecting the out of pocket for that. There's more on reimbursement in other threads.
Make sure the order looks forward. If you are going to need additional joystick/switch control options down the road and/or attendant control, order these _now_ with appropriate justification. If your [dad's] head is already slumping or tilting, make sure something other than a minimal horseshoe head rest is ordered. Lateral and thigh supports should be considered even if the pt doesn't need them yet. A good necessity letter points up the progressive nature of the disease, as well as unpredictable time frames, and points out that "the patient has begun to..." ASL, I think it is, does a lifetime progression drive control package for ALS, though I have not used them.
When on hospice, DME like wheelchairs is handled by hospice so long as it is part of the hospice plan of care. I would think it wise to take delivery of the wheelchair before electing hospice, if possible, since hospice is capitated care and complex rehab equipment orders usually not a part of it. Palliative care that is not yet hospice, everything goes through your current network just as it does now, and hospice, if needed at all, is toward the end of life anyway.