Firstly let me just say PF3 does not use data from Navigraph it uses data from your flight sim, so the runways in use for Luton are 8/26, not 6/24 as you state. Navigraph will be using more recent data than P3D which is using outdates information.
That being said the runway you were given at Luton was correct, according to the wind direction, as there was no AI detected at the time PF3 checked.
12/5/2020 8:39:26 PM: 560 - Extracting Weather Data from EGGW
12/5/2020 8:39:27 PM: 160 - Visibility from weather station: 9
12/5/2020 8:39:27 PM: 160 - Wind DIR from weather station : 198
You say you used ATIS at Luton but that doesn't show in the log at all. Strange!
The runway assigned to you at Manchester was also correct and again it was determined by wind direction.
12/5/2020 8:52:40 PM: 910 - Extracting Weather Data from EGCC
12/5/2020 8:52:40 PM: 910 - Visibility from weather station: 9
12/5/2020 8:52:40 PM: 910 - Wind DIR from weather station : 198
The ACARS Atis report identified the correct runway also -
12/5/2020 8:52:40 PM: 920 - ACARS ATIS Requested:- 'Manchester Airport Information Juliet Weather at 0930 Zulu winds 198 at 8 visibility 9 miles. Sky condition 4 thousand 5 hundred Broken 10 thousand Scattered . Temperature 15 . Dewpoint 5 . Altimeter 1013 Runway 24L in use, Landing departing runway 24L . VFR aircraft say direction of flight. All aircraft readback hold short instructions. Advise controller on initial contact you have Juliet '
Hence you instructions from ATC -
12/5/2020 9:14:26 PM: 180 - Transcript: 'Jersey 017 at Tango November Tango Descend and maintain 3 thousand 5 hundred on 1013 Cleared to final for Sierra Tango Approach runway 24 Left at pilot's discretion Contact Tower on 118.62 when established. '
There was only one problem I noticed and that was on your second ACARS ATIS report where it did indeed show an incorrect landing runway, so I will look into that some more. Having said that there is a major update due for release at the end of next week hopefully so that little glitch may even have been fixed already.
As for AI Traffic using the opposite runway... they got it wrong! I think that's because you have your surface speed set to zero and for some unknown reason if AI Traffic detects a wind speed of zero it wrongly assumes a wind direction of zero (or 360.)
Take a look at this AI aircraft being cleared to land at Manchester -
12/5/2020 9:29:15 PM: 980 - Transcript: 'Pacific Express 7821 Winds 200 at 0 Gusty QNH 1013 Cleared to land runway 06 right '
With winds at 200 you wouldn't be landing on runway 6 would you, you'd be landing on 24L like you were instructed to do.
We don't control AI traffic, that's done solely by the sim and had PF3 detected any AI landing or taking off at the precise time it checked before giving you clearance then you to would have been given runway 6L, which would have been wrong.
So the short answer is, don't have your weather engine wind speed set to zero. If you do the AI traffic could end up landing on the wrong runway and that 'could' be the opposite one to you.