OK - I have checked this and can confirm that this is not related to P3D versions , SDK versions, Third party developers or ADE. First both files you sent me would not initially compile with any compiler due to errors which are not related to scenery objects or buildings. I am not sure how they came to be compiled in the first place. I corrected those errors so that I could compile both airports using ADE 1.79 set to P3D v5. In both cases the default scenery did not show through the airport behaving exactly the same way as the original bgl files and those files compiled with the P3D v4 SDK.
Each of the files you provided contain a large number of user placed exclusion rectangles covering the entire airport, and by chance all the v5 scenery. Neither contain any scenery objects or taxi signs so I assume those provided with the addon are in a separate file.
Those exclusion rectangles when compiled in any compiler and specifically P3D v4 and P3D v5 will exclude the v5 scenery and that is what I expected and saw.
The most likely explanation why you see them if you compile with ADE 1.79 rather than 1.76 is user settings being different in the different ADE versions. There is a setting in ADE which determines whether scenery objects (including exclusions) are compiled with the airport or in a separate bgl file with _OBJ as part of the name. The default setting can be found in Settings > Options > Project
If it is checked then the exclusion rectangles will be compiled to a separate bgl file. If it is not checked then the exclusion rectangles are in the main airport bgl files. That is how they are in the files you sent me.
I can see that if you do have this set for separate bgl files in ADE 1.79 but only copied or added the airport bgl file to P3D v5 then you will see the default scenery as you did. If ADE 1.76 had this option unchecked or you loaded the original file then you will not see default scenery when using that version of ADE.
I am sorry if this is a bit long winded but the bottom line is that it is perfectly fine to use ADE 1.79 and compile your changes for v5 with the v5 compiler provided you have the correct settings or make sure you copy both files into the P3D v5 installation
Of course there could be another explanation that some how in your modification work the exclusion rectangles were removed from the project and therefore did not get compiled at all. There could be other more arcane ways of achieving the results you saw but I would say they would be hard to achieve 'by accident'