It is currently impossible to install using disk druid or kickstart when there already exists a non-Linux primary partition and a standard MBR that you both want to keep. If you don't want to install LILO in the MBR, you need to install it on the boot partition, which is in the situation I described above a logical partition, so setting the "bootable" flag won't work (besides the fact that you can't set the bootable flag via the installer/kickstart). Solution: when a primary partition exists, the installer should create another primary partition as boot partition. Furthermore, the installer (and kickstart!) should have an option to decide whether you want the bootable flag to be set on the boot partition (and the flag should automatically be cleared for all other partitions, of course). Justification: some brand-name PC manufacturers like the use of "hidden" partitions with their "tools" (because they don't want to use a decent BIOS, sigh...) and also supply a special MBR that let you switch to that partition or otherwise use the partition that is bootable.
For cases in which someone wants to determine the configuration of their drives, it is recommended that fdisk be used. We are working to improve the functionality of Disk Druid, but I am closing this bug, as all of the features that you describe are available via fdisk.
But my main problem is with kickstart: this can only use Disk Druid, so I'm not able to use kickstart for those type of systems.
Kickstart now allows the user to specify the partition on which to create partitions, so check out the latest installer. Reopen this bug if you are still having issues with installations.