Disk geometry is different means that the hard disk reports different Cylinders, Heads and Sectors than the BIOS. You can avoid the warning by adding "lba32" to the "lilo.conf" file. LILO will use LBA mode and should not care about disk geometry.
LILO not installed to the MBR is telling you that a "map" file was created for loading LILO. LILO usually stores the sector map in the first hard disk track's unused sectors. You can ignore the warning. If you do things that change the position of LILO's files on disk then you may have to re-install LILO.
Here are some suggestions for you if you do have problems because the first port is being assigned a BIOS drive ID.
BIOS drive IDs are assigned like this.
0x80 First hard disk
0x81 Second hard disk
0x82 Third hard disk
0x83 Fourth hard disk
In the BIOS you can disable the "Auto" disk detection for the first SATA port. Set the drive type to NONE, or in some cases set the parameters to zero to disable detection of any drive on the port.
In the BIOS, make sure that you have the correct hard disk set as the first boot disk. That should assign BIOS ID 0x80 to the first boot disk.
Your BIOS might assign a drive ID to the broken SATA port even though there is no disk attached. In that case you might have a gap in the drive IDs. For example, 0x80, 0x82, 0x83, 0x84 ... You can find out the BIOS drive IDs using a GRUB (0.97 Legacy) boot CD or floppy. Use the "native" command mode from the GRUB boot disk (press "C" at the GRUB boot menu). Then you can enter a "find" command to find a file on one of the disks to determine the disk's BIOS drive ID.
GRUB will print out the names of all the partitions where the file is found.
GRUB assigns disk drive names like this "(hd0)", "(hd1)", "(hd2)". GRUB assigns partition numbers like this "(hd0,0)", "(hd0,1)". For example, "(hd1,1)" is the second partition on the second hard disk (ID 0x81).
Changing BIOS settings, like which disks are enabled for booting, and the boot priority (order) may change the BIOS disk drive IDs. In some cases you may not be able to change the BIOS disk drive IDs except perhaps the first one. Make sure that you have your BIOS set the way you want before installing boot loaders. If you change those BIOS settings you may have to reinstall the boot loaders.
Once you know the BIOS drive IDs you can tell LILO which ones to use if necessary.
LILO example to set BIOS IDs for drives.
Drive "/dev/sdb" in the example is assigned to BIOS drive ID 0x82 instead of the usual ID of 0x81. You have to set LILO's parameters to agree with what the BIOS does. Changing "lilo.conf" does not change how the BIOS assigns the drive ID's. It changes which BIOS drive ID's LILO will use for accessing the drives.
Hopefully you will find that LILO figures out the BIOS IDs correctly and you will have no problems.
Usually, Linux assigns the same device names like "/dev/sdb" the same way every time that you boot. In some cases, removing a drive can cause the device names to change. To avoid a problem in the boot parameters and "fstab" file, use a UUID to identify a disk instead of a device name. If your first disk port stays broken all the time then you should not have trouble with device names changing.
You can also force the device name assignments by editing or creating files in "/etc/udev/rules.d". That should only be necessary if you are running scripts or programs that access devices using the names.