Many 2001 systems have supervised annunciator outputs, including yours. If there was not an annunciator in the system the supervision for the entire panel can be disabled by clipping R8 on the 2001-1007 control module. If the system had an annunciator but not all zones had a lamp the supervision can be disabled by zone. That is done by clipping diodes D19 and D29 on the 2001-1017 zone modules. My documentation has a discrepancy as to which diode is attached to which zone. The schematic shows D19 associated with Zone 1 on the card and D29 associated with Zone 2 on the card. Another memo I have shows just the opposite.
These diodes would also be clipped if several zones were connected to one annunciator lamp. The supervision circuit on the zone card draws a tiny bit of current through the lamp. If several zones were connected in parallel the lamp could glow a little. The the diodes would be clipped on all but one parallel zone to prevent the lamp glow.
Be aware that the raw power module has a bridge rectifier in addition to the transformer. The P2 connector power input to the motherboard is a DC input.
The jumper wires on the motherboard are for some custom operation. There are some black wires that look to be either factory installed or very neat technician work. I will PM some document links so you can figure out what you want to do with these.
A previous picture you posted shows the panel has a OP/SP module in the second row. That was to supervise a second AC power source in a panel that did not have batteries.