If you get rid of the bootable flag you will be all right. Grub does not need a bootable flag to work.
Grub, incase you are worried, is installed on your Debian system.
If you do not want it to boot everything on your drive, installing grub to the / partition is the way to go.
The box in the installer should list all detected OS's when it gets done installing grub on your new system and then wants to know where you want the active part of it installed. Installing to the MBR (Master Boot Record) is best.
You can, however, install to the new / partition. I do this all the time because I use a custom menu that will get copied to the new install after I boot to it from what ever install is handling my grub duties.
When you install to the new / you will not be able to boot to your new install until you boot to what ever install, Ubuntu I assume, is handling your screen menu chores.
After booting to it you need to go to terminal and run;
This will add your new install to the /boot/grub/grub.cfg file.
Installing grub from your new Debian install to the MBR should give you a screen menu containing all existing installs.
If you do not want Debian handling that job from then on simply boot to which ever install you want handling that and run;
sudo grub-install /dev/sdx
where x is the drive designation (sda, sdb, sdi - what ever it is).
That command will simply install the grub from that install on the MBR and when you reboot that will be where your screen menu originates from. Make sure that grub has been updated for that install or you will not include your latest installations.
I have 16 installs of linux on this box spread over 3 drives. There is not one boot flag.