For quick readers, the solution is down below!
Hi Dieter, Wes,
don't get me wrong. I highly appreciate tips and tricks for all kind of things. But, speculating and explaining basics isn't that helpful.
I think Wes has already commented on the matter very well, so I am not going to repeat here.The SWR detection inside amateur radio transceivers is not using an impedance measurement technique. Instead, it uses a relatively simple SWR measurement circuit. Therefore, we cannot expect that "both values should align at least within some khz". Neither can we expect a high SWR measurement accuracy of such in-built devices. Their purpose is related to operational monitoring, especially the detection of antenna faults. We also have to be clear about the nature of the transceiver in-built measurements. Unlike with the FA-VA5, transceiver in-built SWR detection assumes a constant source impedance of 50 Ohms. Surely, common amateur radio transceiver PAs are not able to provide a constant 50 Ohm output impedance. This of course also affects measurements with external VSWR instruments.
Neither was it a disagreement between two devices nor a topic of miscalibration.?Up to 100Mhz it is absolutly uncritical what type of SOL stuff you gonna use. As long as it matches roughly short, open and 50Ohms...
To be clear, if 2 different TRX see 7060khz as lowest SWR it should be the same for the VA5 in scalar mode. Not 7246khz. Neither a poor SWR circuit nor a misscalibration can lead to that offset.
As I mailed with Jan, he directly raised the ground solder point for the BNC connector on the PCB as the most critical part for such failures and wrong values. (I am the second person to report that issue, so don't worry that your device is also affected)
Guess what:

After I resoldered it, the VA5 now works perfectly fine without any deviation from my two TRX. Pls keep in mind that the heat distribution of the PCB requires a
strong 60W+ solder iron to resolder it properly!
As I understand, using wires to bridge somehow the ground point doesn't solve the issue. It is this single point which is important for the accuracy of the FA-VA5.
I checked the connection joints for the BNC connector and they were only partically soldered. So the mechanical bending stress seems to be the root cause. So, if someone is searching for that issues, this might be the solution.
Many thanks to Jan and his promt answers to my mails!
Best 73,
Peer, DL8YF