Likewise, I was confused with your OP... and am still not quite clear. However, I can tell you that By default, our Highlanders (HL) do not come with the Remote Starter from the factory; the Remote Starter is a dealer added assossry item. If your HL was sold to the previous owner with an OEM remote starter installed, you "may be" able to contact (that dealer if you know which one or) Toyota USA with your VIN to find out, that is if there is the OEM remote starter installed by a Toyota dealership at the time of selling your HL NEW.
It is also possible that the previous owner may have installed an Toyota Remote Starter on his/her own after purchased the HL. I would think, unless you take the driver-side lower dash cover/panel and physically take a look, otherwise, we couldn't possible tell you if you have one already installed or not... Perhaps other members have other ways (i.e. Specific fuse to pull/check) to verify.
Lastly, can you contact your Remote Starter installer and check, perhaps the installer incorporated the control of remote starter that you purchased in to your OEM key fob?
There is just one on-board starter circuit, it's hard to imagine that your installer installed a 2nd remote starter unit in your HL without seeing that there is one unit already exists, yet still add-on the 2nd remote starter unit... then again anything is possibles!
Just had an another thought:
1. Remotely start you HL with the OEM key fob, observe how many times the lights flashing and horn beeps, compare that with the remote starting when using the aftermarket controller... If different in pattern, there may just be two system....
2. Have you tried remote starting the engine with the OEM key fob then see if you can shut-off the engine with your aftermarket remote controller and vice versa?