Sorry about the memboot infestation but for what you want to do you need to know about it.
I don't have a computer here with updcd on it but from memory (it has been a couple of years since I last used it) the updated boot disks only appear in the temp dir and are deleted when it creates a CD image. When I first used it I paused the create process and had a look at what was in the temp dir and made adjustments as necessary.
I see that walking_x has given this a test and it works (renaming QSINIT to OS2LDR and including OS2LDR.INI).
It appears that you are now at the position I was a few years ago with creating non standard CD/DVDs of OS/2 which caused me to learn about memdisk to produce no-emulation-boot CD/DVDs. With the work being done on the OS4 kernel, QSINIT, USB and a few other things, it appears that I will have to produce my own updated, enhanced DVD (I already have over 1GB of bits to add to the basic install).