RTS and RTL come with a basic security system. It monitors doors, door locks, hood, trunk, tailgate (swing only), and audio systems. That is about it.
I believe the add-on security system you are seeing is for the RT model only. It seems to operate strictly based on the vehicle's B-CAN bus, so the raw signals for connecting an aftermarket alarm just aren't there.
The factory security system on RTS/RTL is actually part of the driver's door control module, which also houses the power window and power lock controls. It cannot be disconnected without disabling all window and power lock functions. It communicates with other modules of the truck via the B-CAN bus, relaying information about door lock position and buttons digitally.)
Nearly all of the signals needed to control the alarm are available at the MICU, which is part of the same module where the under-dash fuses are located. To get at the necessary connectors, pull off the cover from the left side of the dash (right next to the door), and remove the trim panel at the bottom of the dash. Nearly all of the necessary wires are located in this area. Some are difficult to get at, but this is by far the best place to pick up the signals you need.
The two wires you requested that are not in this area are for factory alarm arm/disarm. These are only inside the driver's door. To disable my alarm, I jumpered across the factory hood open switch, so the factory alarm thinks the hood is open all the time and therefore it will never arm. (I did this in my 98 Accord for 7+ years and it worked great.) I then added my own hood pin switch to compensate for the loss of the factory switch. I recommend this method rather than trying to run wires into the door; it is much easier.
Wire colors and locations:
(First, if you are not familiar with how Honda numbers their connectors, imagine looking into the wire side of female terminals or the male terminals on the terminal side, with the locking release tab at the top. [Gender is determined by the pin terminals, not the connector itself.] Pins are numbered starting in the upper left corner, working across to the right, and then starting on the next row, just like reading a book. Non-existent cavities are not counted, but unpopulated cavities are. Pins are referred to by connector and pin number, such as "P25" below: connector P, pin 25.)
Power lock: (ground to lock), Pink/Black wire, P25 on MICU. "P" is in a 30-pin green connector that is on the tailgate side of the MICU.
Power unlock: (ground to unlock), Pink/Blue, P9 on MICU. Right next to the power lock wire.
Hood pin: (grounded when open) Green/Black, H2 on under-hood fuse/relay box. "H" is an 18-pin gray connector. (Under hood only, raw signal is not brought into the cabin.)
Tailgate pin: (grounded when open in swing mode) Blue/Orange, Q11 on MICU. "Q" is a 14-pin green connector on the tailgate side of the MICU.
Trunk pin: (grounded when open) Blue/Yellow, Q7 on MICU.
Dome supervision light: (ground to turn on) Green/Red, pin 4 of On/Door/Off interior light switch.
Door open sensor: (grounded when open) Blue/Red, pin 3 of On/Door/Off interior light switch. (This is easier than hooking up individual doors, but several minutes after doors are left open it disconnects from ground.)
Individual door sensors: Drivers E15 (Green), Passenger H12 (Light Green/Red), Left Rear E14 (Green/Yellow), Right Rear H13 (Green/White) on MICU. "E" is a 16-pin Light Green connector on MICU. "H" is a 14-pin Light Green connector on MICU.
Horn trigger: (Ground to sound) Green/Yellow in B1 at steering column (under cover). "B" is a 13-pin white connector.
There are possible power sources available in the fuse block if you do not want to tap into a factory wire. Fuses 12, 15, 17 are not used and are always hot. Fuse 29 is not used and is hot in Run or Start.