Hasn't it always been this way?  & supposed to be?  Just like the proto engine, beam & mass driver are available from the start

Yup, i forgot this, i always research Interstellar Travel first so i am used to seeing it by the time i use designer.  Thanks for the correction

If the Prototype Survey Module and the Survey Module were available from the same tech, I don't think that the Prototype Survey Module in its current form would be used. Its only real advantage, aside from being available sooner, is that it costs 24 less base capacity; the lower manufacturing cost, while kind of nice, is also a bit immaterial because 25 manufacturing points off the total ship manufacturing cost is essentially nothing, particularly since the reduced capacity required for the Prototype Survey Module probably means that you're not reducing the cost of the ship so much as spending that manufacturing on something else. The inconvenience of having to pay Thulium for the Prototype Survey Module coupled with the fact that the component is really only a marginal improvement on the standard survey module means that in my opinion there's little good reason to bother with the Prototype Survey Module if both it and the Survey Module are available, especially once other components that use Thulium start to become available (e.g. jamming components). Paying Thulium to get survey ships earlier is worthwhile, but paying Thulium to get marginally better ones? Probably not, especially considering that the computer's survey ships are going to be wasting lots of space on life support rather than on more useful drive components and end their turn each time they hit an anomaly, whether they have moves remaining or not.

Also, you're able to survey from the start of the game, and I wouldn't consider it 'dumb' for a prototype version of a component to become available only two techs (one of which is a specialization, so really the tech that unlocks the Prototype Survey Module is essentially the direct prerequisite for the standard Survey Module) before the standard component becomes available, particularly when developing the tech that unlocks it clearly involves some kind of sensor research (Interstellar Travel also unlocks Interstellar Sensors).

Near as I can tell, the whole point of "prototype" modules is that you get them early, but at the cost of resources.

For instance, the hyperdrive prototype is MUCH better than anything else you'll ever get.  Like, ever.  But it costs Promethion to put on a ship.  Which will add up after a while.

Personally I will be VERY upset if the prototype survey module is taken away from me and put in the middle of the tree.

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Also, as pointed out upthread, Interstellar Travel boosts sensor tech (as well as range tech for that matter).  IT obviously isn't "only" a speed tech, but a sort of "Second Level" of the base techs needed for, well, Interstellar Travel.  One of those Second Level of base techs then is a rudimentary survey module that needs further study before the kinks are worked out.

THAT is what the Interstellar Survery tech is then.  Working out the bugs and making it Mass Produceable from the earlier developed prototype.  Makes even more sense if there are "reports from the field" from ships using the Prototype Survey Module so your science boffins can figure out how to make it streamlined.

Works for me, at least.

Just wondering, if this is your logic, them do you think proto hyper drive, beam & kinetic should not be available  until you research beam weapons // etc?