Saying that some companies are holding back on W10M is certainly true, but I don't think it answers the question as to why universal apps appear to be updated individually by form factor. A few examples:
1)
Testing may be one reason. If you fixed a critical bug that only rears its head on smartphones, and you want to deploy the fix quickly, it may be worthwhile to make that release available only to phones until you've had time to fully test it for tablets and other form factors.
2)
A less dramatic and very common scenario is when a universal app makes use of existing software components which themselves aren't universal. An app that uses one library which exists in two versions, one for ARM devices and the other for x86 devices, is a very common example. Any app that uses such libraries, even if it is a universal app, must be packaged up twice, once for each CPU instruction architecture.
3)
Another example would be that of a universal app that is not a W10 universal app, but a W8.1 universal app, where things work differently (the way milkyway described). In this case the only thing that is truly universal is the app's identity in the store, whereas the binary files that are distributed to devices vary depending on the device doing the downloading. Both types of apps are called universal apps, despite not technically being the same thing.
I'm sure there are many more scenarios where a universal app wouldn't strictly behave like one (as described by the OP).