In my experience the real problem with differing ID numbers in addon missions and campaigns does not come with the basic flying of the mission but when you attempt to go to Advanced Info.  Here are some things to consider.

As you know, when you open any mission where you takeoff or land and you will see a runway entry that looks similar to the ones in your airbases.dat file.  The biggest difference is that the runway numbers in the mission file start at “0” and run consecutively.  So in a mission that uses Henderson the runway number may be “0” while Henderson might me runway number “103” in your airbases.dat file.  That difference doesn’t matter. The key thing to remember about these runway entries in the mission file is that they are not copies of what’s in your airbases.dat file, rather they are copies of what’s in the author’s airbases.dat file.  That’s a key distinction.  Also, you need to know that the game and the Mission Buider (MB) treat this information somewhat differently.

In the game, your starting position and waypoints are determined by the longitude and latitude that’s entered in the mission file.  The runway ID numbers (the 4-digit numbers) don’t necessarily come into play.  You don’t have to have the same scenery installed in your game to fly a mission that I wrote in my game.  That’s a good thing.  I could send you a mission I wrote that takes place in Borneo and even if you don’t have any of the same airbases or scenery in your game you could still fly it.  You might take off and land in an empty field but as long as you have the same aircraft (folder names) in your game and any infrastructure that I added such as ships, buildings, etc. the mission will work.  This also explains why your Lord Howe mission works fine even though the ID numbers are different from yours.  However, as soon as you hit Advanced Info the game may CTD. 

When you click on Advanced Info you are creating a link between the game and MB.  The map you see in Advanced Info is the map from MB.  In MB airbases are identified by what is entered in the airbases.dat file and not what is entered in the mission itself.  In my example above, since you don’t have the Borneo airbases entered in your airbases.dat file when the game (MB) tries to find those ID numbers in the airbases.dat file so that it can display them on the map they aren’t there.  Result – Crash to Desktop.

Unfortunately it is much more complex than that.  As you've found, there isn’t one standard list for ID numbers for every runway in the world, designers can add their own.  Sometimes add-on scenery has an airbases.dat entry that includes an ID number and sometimes they don’t.  As a result, except for the stock runways, we probably all have different runway ID numbers assigned to different bases in our airbases.dat file.  Even if you and I have the same add-on scenery in our games, if my ID number for the runway is different than yours it can result in a CTD. 

There are many different combinations that can cause problems.  For example: none of the ID’s or geographic locations (longitude and latitude) in the mission match your airbases.dat file, some of the ID’s/geo’s match and some don’t, the ID’s match but the geographic locations don’t (the designer and you numbered the bases the same but used different longitude and latitude for the same bases), the ID numbers don’t match but the geographic locations do (the mission starts at Darwin and ends at Lord Howe and both of you have the same scenery but you gave different ID’s to those bases),etc., etc.  In some cases the mission and Advanced Info will work if the takeoff data is correct even if the landing airbase information is different.

Suffice it to say that these conflicts between the ID numbers and runway locations in missions and what's in your airbases.dat file can cause:
1)      no problem
2)      a mission failed to load error message
3)      a CTD when you start the mission; or
4)      a CTD when you hit Advanced Info.

The bottom line is that any time you encounter a CTD when hitting the Advanced Info or starting a mission, especially if you are flying an add-on mission, always open the mission file and check the airbase info first.  To fix the problem you need to make sure that the ID numbers in the mission don’t match any that you have in your airbases.dat file. If you find a match, change the mission ID number to one that you aren’t using. 

You can also get a CTD on your own missions when you have duplicate runway ID’s in your airbases.dat file.  That can happen easily as you add airbases.  Always do a search of the file for the ID number you are entering when adding a base before you save the file.  It might save you grief later.

Hopefully some of this will help you on your quest to solve the runway ID issue.