You've just started. You are still in the first tech age. Those technologies are in the second age. Check the bottom of the screen bars.

Ok the techs look like these ones are unlocked by certain abilities. 

It's a combination of being a starting tech based on your ability, and not having unlocked the age yet. From my perspective it doesn't look like a but. 

What are all your species abilities.

Without having a computer screen in front of me right now I'm guessing your the Thalans, or at least Time Travelors.

I think game wise it would be better if the starting techs weren't ever on the trees.

I'm not understanding you unlocking all the t ch ages. Your pictures on the bottom of the screens clearly show that you started the first tech age. The techs you are looking at are starting techs. Both techs are in an age you haven't unlocked yet according to the tech age bar at the bottom of the screen. You get the starting tech, but you are not in that tech age. 

You should be able to build large scale ships can you build them.

I do not see the issue in the screenshots (Not checked the saves requires to much work, removing all my mods etc ).

You have picked Time Travellers as an ability and get these 3 techs for free, they show up grey (Any tech age you are not in has a darkened tint added too it) in the screen shots because you have not progressed into the tech ages required for these techs, cause you got them for free.

If they are still grey after unlocking the tech age req's, that is an issue and probably linked to the bug that causes techs to lose thier color and turn white.