This may be a good time to mention that DFSee has a modified OS/2 boot loader that raises many limitations including the number of boot entries and LBA support.
I am using it on the Book386 to boot DOS/Win3.x, Win95, NT 3.51, OS/2 Warp 3, FreeDOS, and several Linuxes from a single 16GB CF card.
The partition layout is 3 primary partitions (OS2BootMgr, a DOS FAT16 one, a Win95 FAT32 one) and logical partitions for the rest of OSes (NTFS NT one, HPFS OS/2 one, FAT32 FreeDOS, ext2 for Linux, etc.) .
All of them can launch directly from the OS2BootMgr menu.
Because the Book386 doesn't do LBA, I am using Ontrack as DDO. (Ez-disk is probably easier to work but I conceptually prefer the "shifted disk" approach by Ontrack as it allows most real mode bootloaders to work unmodified; on the other hand protected mode bootloaders and OSes need changes, but most era OSes do support Ontrack natively).
So for example, to boot OS/2, the chain goes something like:
BIOS -> Ontrack MBR (provides int13) -> DFSee-installed MBR (int13 capable) -> DFSee-installed OS2BootMgr -> DFSee-installed VBR in the OS/2 partition (int13 capable) -> OS/2 kernel (updated with latest fixpack since I think original one doesn't use int13).
DFSee itself is immensely useful to debug this monstrosity, it will show which boot records you are using all along the way and always install LBA-capable ones. It also allows you to avoid the very-fragile OS/2 Warp 3 FDISK.
Suffice to say that booting NT from a logical partition is possible and trivial, many bootloaders can do this on their own. The OS/2 boot manager is however stupid when it comes to NTFS partitions, so you have to apply the "hidden sectors" trick manually - but just once. (DFSee doesn't do that and worse: its "fix partition table" command will undo this trick).
It is booting from an OS/2 logical partition that is a bit more convoluted, as far as I remember OS2BootMgr is the only period-correct boot manager that can do it. And even from recent bootloaders I am not sure which can do it natively; I have patched GRUB4DOS in the past to do it, the OS/2 boot protocol is very well documented.
I am quite sure you'd likely have no issues booting the DOS OSes from a logical partition either. But it's nice to keep something that can be "natively" booted to diagnose problems.
That said I think the bootloader is not really that important piece here and most of the time you are going to be fighting the stupid idiosyncrasies from the various OSes. E.g. OS/2 Warp 3 outright refuses to show any partition over the 1024 cylinder limit as installable (even on Ontrack systems). NT refuses to install to logical partitions, and is so crappy overall that sometimes NTLDR and the NT kernel will disagree on how to number the partitions you have, leading to disaster. Even the latest official updates are not enough, only the Win2k boot sector and NTLDR can seemingly boot from LBA/Ontrack, and on NT 3.5x you need a patched atdisk/atapi.sys for LBA support too. So be ready to be "transplanting" OSes from temp installs to your final disk a lot (plant analogy really appropriate here).