The increase in per unit cost probably would be entirely insignificant and minuscule compared to the revenue they'd lose by not being able to charge predatory prices for storage upgrades. So it would be a secondary or a tertiary concern at best..
What they/everyone really ought to do is to standardize that, with the flash chips themselves still connected via a modular connector and the "NVMe controller" as open source.
Imagine integrating the flash ECC/RAIN with ZFS et al. Or the ability to decide for yourself if you want a lot of QLC or a bit of SLC or a mix of both, in software at runtime.
At least some portion of an operating system's bootloader chain must be installed to the internal storage, because that's all the firmware knows how to read (unlike Wintel PCs where there's a UEFI driver providing USB storage stack support). That bootloader running from internal storage is then free to enumerate external storage devices to locate the rest of the OS it is trying to load.
Irony, of all laptop I have owned, the most problematic was the Apple PowerBook. It's screen became defected a month or two after the warranty ended. The external VGA connection had issues and might require a couple restarts to get a signal. It could barely be used as a desktop computer. Even though I used it to write my first production software solution. It was ditched as soon as financially possible.
Soldering them to the board is just an asshole thing to do though, especially since these machines can't boot off of USB if the NAND dies. Surely some elastomer BGA sockets wouldn't cost that much. There's no sane explanation other than they're doing it so you have to buy a new Mac to get more storage.