The SD Card Association (who define the SD Card Specifications) mandate the use of exFAT for cards larger than 32GBytes. To be compliant, card manufacturers must ship according to these file system format specifications (and compliant host devices must adhere to the formatting guidelines) so will certainly not default to NTFS and are also very unlikely to test their cards with NTFS. That's not to say that you can't put any file system on you like, but due to the nature of flash based SD cards you are likely to increase your risk loss of data or corruption if you deviate from the defaults.
Regarding allocation unit size, the best setting for this is very closely linked to the geometry of the memory card (specifically the write and erase unit size of the underlying flash memory that the card uses), and needs to be matched for best performance and reduced wear. Again, the standards try to ensure that the host and card plays together nicely to make sure that these settings are optimal, and putting a different file system on top is likely to reduce it's life and performance.
The SDA even provide a formatting tool to ensure that you're using the optimal file system format and layout for your card:
SD Memory Card Formatter 5.0 for SD/SDHC/SDXC
(this is general advice though, in your specific case if you just have a read only ISO then you may not encounter issues)
