I calculated the same 2Wx1H mosaic of NGC5139 layout using Telescopius. Interestingly it generated :
Pane, RA, DEC, Position Angle (East)
PANE 1, 13hr 29' 07", -47º 28' 46", 0
PANE 2, 13hr 24' 27", -47º 28' 46", 0

These are 4' 40" apart in RA. Compared to 3' 10.7" apart from the Ekos tool. The Telescopius panels line up correctly when checked in Stellarium.

As the DEC calculations are OK, I wonder if the issue relates to the difference in units used between RA and DEC - maybe the code behind the tool is treating these the same where they should be different?

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