I'm. Not a modder, but can't. You just move the tech at the beginning of the tree. Also isn't. There an ability to start out with techs. Maybe this can be modified to include planetary invasion. Also if you do this for your custom race then you should do this for all races. Don't. Forget to reset your tech points to 0.

I want to make sure we are on the same page here before I start offering suggestions.   Did you try to modify the following stat block (TransportModule found in ShipComponentDefs.xml)?

<ShipComponent>
<InternalName>TransportModule</InternalName>
<DisplayName>TransportModule_Name</DisplayName>
<Description>TransportModule_Dec</Description>
<ArtDefine>Transport_01</ArtDefine>
<Category>Modules</Category>
<Type>TransportModule</Type>
<PlacementType>Module</PlacementType>
<Stats>
<EffectType>Value</EffectType>
<Target>
<TargetType>Ship</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>10</Value>
</Stats>
<Stats>
<EffectType>ManufacturingCost</EffectType>
<Scope>Queue</Scope>
<Target>
<TargetType>Ship</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>27</Value>
</Stats>
<Stats>
<EffectType>SupportMass</EffectType>
<Target>
<TargetType>Ship</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>25</Value>
</Stats>
<Stats>
<EffectType>CanInvade</EffectType>
<Target>
<TargetType>Ship</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>1</Value>
</Stats>
<Stats>
<EffectType>PopulationCap</EffectType>
<Target>
<TargetType>Ship</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>3</Value>
</Stats>
<Stats>
<EffectType>Maintenance</EffectType>
<Target>
<TargetType>Ship</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>0.25</Value>
</Stats>
<Prerequ>
<Techs>
<Option>PlanetaryInvasion</Option>
</Techs>
</Prerequ>
</ShipComponent>

And change 

<Techs>

<Option>PlanetaryInvasion</Option>

</Techs>

to

<Techs>

<Option>RaceFluffPlanetaryInvasion</Option>

</Techs>

While also changing 

<InternalName>TransportModule</InternalName>
<DisplayName>TransportModule_Name</DisplayName>
<Description>TransportModule_Dec</Description>

But leaving 

<Type>TransportModule</Type>

alone?

I'm busy on my mac side of my computer, so I can't look at this for a while, but it seems to me that this should work.  

What exactly is the game saying when you try to invade a planet?  Does the ship say it can invade planets as one of its abilities when you get the info for it?

And is there anything interesting in the debug.err file when you try to invade the planet?

====

Alternatively what you COULD do is just change the prereq for the Military Academy to something else that all the other factions get and then in turn make sure that either your custom race doesn't get that tech, or you create a race specific version of it without the Militarty Academy.   

This is more or less what I was suggesting.  In ImprovementDefs.xml change the xml for MilitaryAcademy from:

<Prerequ>
<Techs>
<Option>PlanetaryInvasion</Option>
</Techs>
</Prerequ>

to 

<Prerequ>
<Techs>
<Option>SomeOtherTech</Option>
</Techs>
</Prerequ>

With "SomeOtherTech" being just about anything in that area.  My rationale is IF planetary invasion is hard coded, then simply attach the Military Academy improvement to something that isn't hard coded and make a fluff version of that tech for your custom race so they won't get it whilst everyone else will.

You shouldn't even need to change any of the other races since they'll follow the xml def in ImprovementDefs.xml.

That's the workaround that immedately comes to mind.  Basically nothing says that the Military Academy HAS to be attached to the Planetary Invasion tech.  As long as it is more or less researchable at the same point in the Military Tree and the tech is available to everyone else, I don't see a particular reason why it can't be shifted.  Annoying that one has to do this, yes.  But that's why it is called a workaround, I suppose.

This does sound like a bug, so perhaps you should send a ticket to Stardock about it.  I am curious though if the ship itself says it can invade planets when you click on it/pull up details about it.  If it doesn't, then perhaps something is wrong with the XML parsing somewhere.  If it does, then it is very probably a bug and something SD should be made aware of.

Simple answer that should work, though i'd need to test it to be sure, add a preclusion specifying the relevant tech tree of your race to the military academy.

I decided to make a ticket:

#URG-630-11157

But I would imagine this kind of thing doesn't get as much of a priority as fixing vanilla game issues, understandably so.