One thing I've noticed about both FSX (and P3D also) is how outdated the airport and navigation data are -- for example Coronado Airport (K4AC) in Albuquerque is long gone and the Sunport (KABQ) no longer has Rwy 35/17, Double Eagle (KAEG) now has a control tower, radio frequencies have changed, and so on.  

I've used this to update nav data in FSX/P3D

https://www.aero.sors.fr/navaids3.html

Here's my question.  Some aircraft have appear to have nav instrumentation problems (VORs out of position, radials misoriented) and some don't. Which data actually come with an aircraft (like the Carenado version of the C90GTX) and what does not? What's the best way to make everything up to date as possible or at least consistent?

If you have aircraft addons that support navigraph or nav data pro, then you can subscribe to one of those services to get updates for those aircraft. However the default data remains dated and this won't help you with navigation using radio beacons. If it's an option, downloading or buying scenery for the airports you fly to will help in some ways as well.

You are not going to get it consistent, unfortunately..

Best you can do, is update one component at a time, as you are doing.

For individual airports, you can make manual changes with tools like ADE.

An addon GPS or FMS typically comes with its own navdata file which tends to be of a

different date than the scenery you are flying over.. so it is not always going to match up.

Thanks.  I've been using the real life Avare tablet GPS navigation program with FSX/P3D as well.  That's how I noticed how much things were off.