Besides Linux, I'd imagine this is going to be a problem for bootable recovery and firmware update utilities.
For example, many data recovery products require the user to boot a CD or USB for it to retrieve data from the unbootable operating system, such as in the case where the hard disk has bad sectors.
Many disk cloning products also require the user to boot a disc to clone the OS partition, such as when migrating an existing OS from a hard disk to an SSD. Of course the main users affected will be those buy a laptop, which generally does not come with recovery media to reinstall the OS. Even if the user uses the Windows backup utility, the replacement SSD will need to be at least as large as the original hard disk for the restore process to work, which is a problem with most laptops coming fitted with a 1TB hard disk.
Although not as common now, some products still require firmware updates to be carried from a bootable disc.