I think I understand your question
Your dealer told you that both of the CD changers are for the LX only? While I believe the "in-dash cassette deck" is for the LX only (EX already has one built into the radio anyways). To my understanding the "in-dash CD changer" probably won't work on the EX, but the "under passenger seat CD changer" should definetly work on a non-LX. While I would have guessed the "in-dash CD changer" would install fine on an EX-L in the spot used for the DVD player on a EX-RES, the installation instructions clearly show it being installed right under the smaller radio used on the LX. My quess is that it'd physically install fine....but the cables aren't wired up for that option. But that's just a guess..I don't have the Repair Manual in front of me. A clever technician could probably wire it up with some kind of extension harness...but it wouldn't be as per the Honda installation instructions. However, if you look at the installation instructions for the "under passenger seat CD changer", it clearly shows how to install it in a NAV and non-NAV Pilot. If this changer was ONLY meant for the LX...they wouldn't show how to install it in a NAV Pilot. I didn't study the instructions beyond that, but I think that's enough info for you to dispute your dealer. It COULD be the case that it will work in the LX, AND EX-NAV, but not the EX-L or EX-RES. So if I understand you properly, the "under passenger seat CD changer" is totally acceptable to you. I would restate your request to your dealer asking him to take another look at the installation instructions for the "under passenger seat CD changer". Good luck to you.
Note: When I refer to the installation instructions, I'm reading them (in PDF form) right off the collegehillshonda website.
Note: Hmmmm....looking at the instructions more carefully it looks like it's an "under driver seat" install.....not "under passenger seat" like I had be lead to believe. But either way....still sounds like it's what you want.
