That's one of the reasons why EFI/UEFI suck. (the boot system PCs use now in place of old BIOS/MBR system)
Windows and Mac OS do hide lots of stuff on these partitions and you can't do jack about it.
The missing space isn't the UEFI. UEFI BIOS is still BIOS, the hard drive is still GPT or MBR, even if it stores the UEFI on the hard drive, it's a very lightweight system. On top of that, having a bridge between the BIOS and OS gives OS based malware protection the ability to detect and quarantine even rootkits.
It's not like it's extra space, either, it's just part of the space that it used to use for the OS partition is now off limits for obvious reasons (GPT/MBR can't be corrupted by other failures or malicious software). They also separate the OS partition from the Data partition and the Recovery partitions. They even go as far as to segregate "owner" accounts from the system admin account specifically to limit access to the root to any malware the person might unintentionally install.
You might lose visibility for a small portion of your drive under the new systems, but they are functionally much better than the older ones.