Well, yea - it's annoying and weird.
On XB, using the default context for XB controller, the primary is on the right trigger and the secondary on the left trigger, which is the correct match for hud / controls
But using the kb/m, the consistency goes down the drain - yes, in the windows world, left mouse button is the Primary while the right mouse button is the Secondary
So yea, It's very dubious to have the primary fire-group displayed on the Right side of the HUD, while having the primary fire-group trigger on Left mouse button
It's like the hud/controls were designed to be used with a Controller, but then they decided to add kb/m as well
I mean, the right hand Index finger (also known as trigger finger) is the Primary actuator (even for me, a leftie) so it makes sense for a controller to use that finger for primary Fire trigger.
The same index finger is also the finger used in the windows world for mouse primary button, the Left button, while the Right mouse button is a secondary button
Which means it's perfectly normal to have the left finger triggering what is known as the Primary Fire control trigger, but this yields conflicting results in having the HUD matching the Inputs when using controller versus mouse
My experience was really nice when i started to play ED on XB using a controller, but then It felt really weird when one year later i started on PC using the kb/m and it's still weird now, 3.5 years after i started on PC.
The solution is indeed to set the:
- Primary Fire to Mouse 2
- Secondary Fire to Mouse 1
which also look/feels weird
So, OP, you really need to pick your poison, that is to be annoyed about either:
your primary fire is set on the secondary mouse button (this is kinda poking at my OCD)
or
the hud displays primary on the right while you press the left button (and this again is poking at my OCD)
(Edit: and no, renaming the Primary/Secondary to Left/Right won't work since it will annoy the hell out of Joystick users

)