To me, the most obvious reason for Canon having an extra SKU is simply that it allows them to charge more for CLOG out of the box. Some people who want CLOG would pay more for CLOG pre-installed, even if the upgrade were free but required a visit to the Canon centre. That might be because there's no Canon centre nearby, because it's not worth their time (if it's a corporate device, for instance), because they're impatient and want their new toy NOW, or because $300 just isn't that important to them one way or the other.
Heck, some people would pay more for CLOG preinstalled, even if you could download it and install it yourself for free. You see that all the time in PCs.
In terms of inventory at local camera shops, I think that isn't a problem. Most camera shops aren't going to have more than one or two 5D4 on hand anyways, because it's not like they're going to sell three of these in a day on most days. They can almost always get one sent out from a local Canon warehouse, which won't take long -- so the onus is on Canon to stock their shelves, not the dealer. It's a low risk anyhow, because someone who wants a 5D4 NOW may take either the more expensive model, or the less expensive one and deal with the upgrade, unlike 5DS/R where it's not like you can add (or take out) the filter after, so the wrong model on the shelf is likely useless to the buyer.
The other reason to have separate SKUs is that it lets them discount the non CLOG version for people who will never shoot video anyways. And finally, it also gives Canon some additional insight into what 4k is worth to people, based on the upgraded model sales as well as the upgrade ratio of existing devices. I have suspected that one reason to do it in the Canon Centre is that this allows them to track which devices are upgraded, and which are not, which gives them a good handle on the ratio of stills-only shooters who are on the 5D4 platform. I think that's a valuable piece of information.
Never thought this day would come
