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Is there any reason why it might be a bad idea to take programs that are typically installed as bootable USB drives and instead create an appropriately sized partition for each of them on the internal drive? The obvious upside is that they would always be present, no hassle of keeping track of thumbdrives; it's basically just multibooting at this point. These programs also don't tend to take up very much storage space, so I don't imagine that it would be a significant loss of space on the internal drive.

Are there any obvious downsides that I haven't considered? (Besides the worst-case "internal drive corruption" situation, for which I would want to make a separate rescue disk regardless)

ETL
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Actually GParted is not in the same category as Memtest86+. The only versions of GParted that I have used were a Linux application that requires a running Linux OS with GUI. The only versions of Memtest86+ I have used were standalone programs that ran from a boot menu, and required no OS or kernel.

GParted is an application program that requires an OS. It is not a standalone program. GParted Live is simply the GParted program bundled with a Linux Live CD/DVD/USB image. The documentation clearly confirms this, and shows the graphical desktop and other available applications, such as a web browser and terminal. enter image description here

If you have doubts that GParted Live is not a standalone program, then you need to boot a GParted Live image. Then open the Terminal application in order to access a shell.
Type uname -a to list the Linux kernel build information. A standalone program would not incorporate a Linux kernel.
Type ps -a to list all the Linux processes currently executing. A standalone program would not have a scheduler running other programs.

FYI a Linux Live CD/DVD/USB image normally exists as a single executable image file. When the Linux OS boots, it uses an initramfs (a special type of filesystem in main memory, somewhat similar to a RAM disk) for its root filesystem. Such an implementation of Linux does not require any drive/disk partition to operate.
Hence your proposal to allocate a partition for each boot choice is unnecessary.

To accomplish various boot choices, you only need a custom boot menu (e.g. using GRUB) and a boot partition or boot directory in a partition. Memtest86+ and a LiveCD/USB image (that may feature a headliner app such as GParted) can each be stored and booted as a simple image file.

A GParted Live image could be a suitable starting point, especially because it has the configuration options available for the GUI at boot time. Expanding the boot menu to offer Memtest86+ should be trivial.
Adding other boot choices could be as easy if they are truly standalone programs. But if the program is another Linux application, then the ideal solution would be a (complicated?) rebuild of the Live image to incorporate that Linux program.

sawdust
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Partitions as such for software of the kind that requires disks to be in "not in use"-state might be one option.

But even easier is using a tool that creates "boot options" of ISO files, i.e. bootable OS-image files.

One such is https://grml.org/ which will allow ISO-files residing in /boot/grml/ to be booted. e.g. you can run your clonezilla (ISO-image) by just selecting it at boot time, freeing up your system's partitions for clean backup creation... and similarly for manipulation and repair of partitions with gparted and ddrescue.

$ dpkg -l | grep grml
ii  grml-rescueboot                               0.5.0                                      all          Integrates Grml ISO booting into GRUB

so:
$ sudo apt-get install grml-rescueboot
... will install a version of it, on Ubuntu's

Hannu
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