While i know some things, i would love to get it explained step by step, or something similar, as to how the Devs achieved this. Eventually, people are going to want to do this. I figured i might as well ask. 

Chiming in with Painter448, there's a couple of different ways to go about this. Adding IsLargeSlot="true" makes the circle to drop the weapon/module into large. In addition, you need to add another line further down. Here's an example weapon slot from the XML:

<WeaponSlot Name="Weapon01" ShowPositionMarker="true" PositionMarkerAngle="180" IsLargeSlot="true">
    <LineOfSight>
            <Direction X="0" Z="1"/>
            <Angle>270</Angle>
            <VisualSlotName>MDL_Wp_Small_Up_00</VisualSlotName>
    </LineOfSight>
    <ModuleModifier>
            <SimulationDescriptorReference Name="TopWeapon"/>

            <SimulationDescriptorReference Name="MultiplierX2"/><!--This line is what changes the weapon to do twice the damage, at twice the build cost-->
    </ModuleModifier>
    <UISlotName>UIBackWeapon07</UISlotName>
</WeaponSlot>

Coding XLM wise i can acheive the effect desired. But im talking a bit more than that. If you change the coding, then the model, animation, and what you would expect appear in the slot in-game, does not happen. When i have attemped the above, the gun is turretless, but still operates in combat. I am assuming there is something additional to get the model to generate.

This line determines what model shows up, and as far as I can tell, is specific to the ship model and faction:

<VisualSlotName>MDL_Wp_Small_Up_00</VisualSlotName>

In other words, you would use the VisualSlotName that was already there for the model and animation. I'm fairly certain they can't be changed at the moment. 

Which faction, ship and slot are you trying to change?

Take your pick really. I haven't got anything specific in mind. I was in EA trying to do this to the Vodyani support frigate, but gave up as it was EA1 and people were uninterested then.

Alright, so the Vodyani hull descriptions are in the following file:

\Steam\steamapps\common\Endless Space 2\Public\Simulation\Battles\HullDefinitions[Vampirilis].xml

The small support hull is labelled: "HullSmall02Vampirilis"

This ship only has one weapon slot. Here is the original code:

<WeaponSlot Name="Weapon01" ShowPositionMarker="true" PositionMarkerAngle="180">
    <LineOfSight>
            <Direction X="0" Z="1"/>
            <Angle>270</Angle>
            <VisualSlotName>MDL_Wp_Small_Up_00</VisualSlotName>
    </LineOfSight>
    <ModuleModifier>
            <SimulationDescriptorReference Name="TopWeapon"/>
    </ModuleModifier>
    <UISlotName>UIBackWeapon07</UISlotName>
</WeaponSlot>

Option 1: Updated code to change the visual of the slot size and weapon will cost x2 and do x2 damage:

<WeaponSlot Name="Weapon01" ShowPositionMarker="true" PositionMarkerAngle="180" IsLargeSlot="true" ModuleCostMultiplier="2">
    <LineOfSight>
            <Direction X="0" Z="1"/>
            <Angle>270</Angle>
            <VisualSlotName>MDL_Wp_Small_Up_00</VisualSlotName>
    </LineOfSight>
    <ModuleModifier>
            <SimulationDescriptorReference Name="TopWeapon"/>

            <SimulationDescriptorReference Name="MultiplierX2"/>
    </ModuleModifier>
    <UISlotName>UIBackWeapon07</UISlotName>
</WeaponSlot>

Option 2: Updated code so weapon will cost x2 and do x4 DPS with better cooldown:

<WeaponSlot Name="Weapon01" ShowPositionMarker="true" PositionMarkerAngle="180" IsLargeSlot="true"  ModuleCostMultiplier="2">
    <LineOfSight>
            <Direction X="0" Z="1"/>
            <Angle>270</Angle>
            <VisualSlotName>MDL_Wp_Small_Up_00</VisualSlotName>
    </LineOfSight>
    <ModuleModifier>
            <SimulationDescriptorReference Name="TopWeapon"/>

            <SimulationDescriptorReference Name="LargeWeapon"/>

            <SimulationDescriptorReference Name="MultiplierX2"/>
    </ModuleModifier>
    <UISlotName>UIBackWeapon07</UISlotName>
</WeaponSlot>

Option 2: Over the top...weapon will cost x4 and do x8 DPS with better cooldown:

<WeaponSlot Name="Weapon01" ShowPositionMarker="true"  PositionMarkerAngle="180" IsLargeSlot="true"   ModuleCostMultiplier="4">
    <LineOfSight>
            <Direction X="0" Z="1"/>
            <Angle>270</Angle>
            <VisualSlotName>MDL_Wp_Small_Up_00</VisualSlotName>
    </LineOfSight>
    <ModuleModifier>
            <SimulationDescriptorReference Name="TopWeapon"/>

            <SimulationDescriptorReference Name="LargeWeapon"/>

            <SimulationDescriptorReference Name="MultiplierX4"/>
    </ModuleModifier>
    <UISlotName>UIBackWeapon07</UISlotName>
</WeaponSlot>

Note: Regardless of the code, the animation for the weapon doesn't change. 

Hope that helps,

Knyghte.Fall

Ill look into it, and play around with it. Thanks.