First thing is to understand what those other states allow. Since you say "agreement with" I have to assume you're talking about a CHL and for most practical arguments, a CHL won't have anything to do with carrying a handgun in/on a vehicle.
If all you're asking is how can you secure a handgun on a bike, you ought to rephrase the question and leave out any talk of agreements or legality and stick to the logistics of securing a handgun because regardless of where you are, making sure it's secure and safe is all the same. The legal requirement of how it can be carried is a whole other discussion.
ck the NRA site, they have the rules for each state .
you probably want to get a cable lock or something similar to lock the gun unusable, in some states. they require locked up and unloaded,
I personally wouldn't leave my gun on my bike in my bags locked or not,
I would rather carry the gun locked in my backpack and ammo on the bike.
if I had to disarm.
I have a cable lock i can run thru the barrel and lock,
kinda like they do the zip-tie thing at the gunshow.
Generally speaking, if I can't carry I won't travel that state. Many of them offer "work-arounds" in terms of securing the gun so that you're compliant with the law. Of course, since we tour on an Ultra w/a trailer behind us, our storage options are fairly broad. I've even gone so far as to disassemble the gun and store the various components in different areas of the bike/trailer.
Its a tough question to answer because you'll need to verify with each state how they define "in" on a motorcycle.
Your best bet before traveling is scope out that particular state's rules.
If I wasn't able to do that my course of action would be to unload the gun, remove mag and put the gun in my luggage and make sure the luggage is pretty secure to the bike and not take it out until I got the privacy of a hotel room.
This is a question with 50 different answers. The general answer is, as mentioned, secure the weapon, either with a cable lock, zip tie, or in a locked case. Be sure it's unloaded and the ammo is stored separately. You should do some research to find what the EXACT laws are regarding motorcycle carry in the nonreciprocating states.