Issues arise because using this method is a silent way of changing weapon modes, using the regular defined method clicks (audio bugs noted already about hearing weapon mode switching from 200+ meters).
There are also animation bugs relating to use of the Change Gunner Weapon method.
Using this method you can change weapon modes while reloading, but not while aiming down sights.
The largest of the issues pertains to a combination of the previous two problems.
If you use this method of weapon firemode switching during a reload (often done in moments where you need to swap to full auto while reloading and near enemies in my experience), you can bug the reload animation in a very particular way: weapon firemode switching after that reload, both normally and using this silent method, cause the weapon to switch to it's mid-reloading animation state. This means that switching weapons not only changes the firemode switch position but also can make a weapon appear as if it has it's slide pulled back permanently, or in the case of the Zafir 7.62 LMG the magazine box is entirely missing from the weapon.
Issues relating to this are fairly minor on most weapons from my testing (aesthetics and minor ones at that), except with the Zafir 7.62 LMG. The Zafir suffers from this animation issue the worst because of the plate over the chamber flipping upwards in the middle of the reloading animation and the magazine vanishing entirely.
Doing the silent weapon mode switch during a reload, and then switching fire modes also interferes with the Zafir's iron sights, ACO, RCO, ARCO, MRCO sights, and potentially more. Long range sights such as the thermal, NWS, and LRPS seem unaffected due to camera placement on the weapon being forwards of the plate. This plate stays up until the weapon mode is switched again by either of the two methods, blocking all view and essentially making any aiming down sights during one of the two modes entirely pointless.
However, it is possible to fix this issue by dropping and picking the weapon back up off of the ground. Reloading without swapping firemodes, switching weapons, and a few other combinations do not seem to fix it consistently, though occasionally they do manage to break whatever is holding the weapon in it's animation state.
It is unknown at this time if these animation issues are client-side only, or can be seen by other players on a server.