These types of modifiers have to go into the sovereign's traits for some reason. A word of caution though, those buildings will boost the tile yields of the terrain around them - potentially creating very, very good starts.

Another option you could pursue is to create a new once-per-faction building that does what you want, and is unlocked from the faction trait. The player then builds it as soon as the game starts. A bonus of using this method is that the building, if captured, will be razed so you can't rush the AI for it.

You champion, that works a treat (using the building method).  Not exactly how I would have liked it but it's a pretty darn good alternative, thanks.    

    <GameModifier>
        <ModType>Player</ModType>
        <Attribute>StartPositionHasResource</Attribute>
        <StrVal>Wild_Dragons_Liz</StrVal>
        <Radius>3.0</Radius>
        <Provides>When the Lizardmen hid in caves beneath the earth, one of their kind brought back dragon eggs after meeting a dragon. The eggs have been stored since then...

Faction starts with a Dragon Cave within 3 tiles of starting position. Faction still requires the normal technology to use the resource.</Provides>
      </GameModifier>

Check out the Dragonkind sovereign trait for lizardmen, it works in vanilla 1.12.

No, it may be outside visual range.

No, the radius tag is not ignored. I tried this out myself, and it is working properly. But a radius of 3 allows the resource to be placed outside of initial sight range of your sovereign.

Well you got me curious.  I tested this, I found that I got the free resource on 6 out of 10 times.  Weird.

I created this ability based on HF's Lizardman code:

<AbilityBonus InternalName="BeeTestAbility">
   <AbilityBonusOption InternalName="BeeTest">
   <DisplayName>Free Bees</DisplayName>
   <Description>Free bees!</Description>
   <Icon>Ability_Adepts_Icon.png</Icon>
   <GameModifier>
      <ModType>Player</ModType>
      <Attribute>StartPositionHasResource</Attribute>
      <StrVal>Resource_TwlightBees</StrVal>
      <Radius>3.0</Radius>
      <Provides>Free bees!</Provides>
   </GameModifier>
   <Cost>1</Cost>
   <HideWhenUpgraded>0</HideWhenUpgraded>
   <AIData AIPersonality="AI_General">
      <AIPriority>5</AIPriority>
   </AIData>
   </AbilityBonusOption>
</AbilityBonus>

Then added it directly to one of my custom sov's as he specified using this:

<SelectedAbilityBonusOption>BeeTest</SelectedAbilityBonusOption>

Then I regenerated the map 10 times, and found that it usually works (6 out of 10 times).  It definitely doesn't always work.... I can't spot why.  Possibly depends on the stamps or surrounding terrain maybe.

Out of interested, HF's workaround he provided me above (to unlock the free resource from an improvement) has never failed for me so far... so it seems to work reliably.  If you want to play with free resources it might be better (i.e. more reliable) to unlock them using an improvement... it could be a really cheap one that can be built on 1 turn.