Ditto as Teeo noted and more.
With more content to feed tech specializations, we should find players taking differing angles of the same trees. Specifically I’ll play off your examples (they’re good ^_^).
Within the same tree, one player might develop techs for constructing the most heavily modified battleship hulls. He can trade those away and they’ll retain the extra armor, slots, etc (each modification has its own tech with multiple levels and appropriate construction costs and upkeeps for the owner). Another player might delve into producing them cheaply and quickly without the modification, instead he stacks techs that reduce costs, increase construction speed and possibly even remove slots or armor to deepen the discounts. With the tech to reach these tiers the prices of research within the tree have dropped a significantly.
A player might go for the best modification techs and the efficiency techs. If he does, the investments into the tree have by then heaped ugly boosts to the cost of tech advances related to mining, governance, weaponry, engines, planetary construction, troop and crew training, etc. The player fully immersed in a fleet building tree to perfect his speciality must rely on trading his works away for the support of others. He likely has first-hand access to only the lowest tiers of tech outside that tree but can make steady progress up another as it accumulates its own tech discounts and further boosts tech costs outside these two trees.
If he can’t mine fast enough for production, that’s fair and good. He’s forced to trade or raid for resources.
Mining, as I hope to see it, should have four direct influencers and many indirect. Density foremost decides the rate. Structures, the mines themselves being modified by tech in a tree of planetary construction, then determine what is pulled from that density. These two are tradable. What are not (yet) tradable are tech advancements that further modify mining both by researching boosted mining methods and by modifying the workforce morale. A player could plausibly pursue depths of tech in two of the three (planetary construction, mining, governance), but if he fully immerses his empire toward this, he will likely need to trade for support from others. Planet building and gifting can be an avenue all its own, leaving the builder defenseless unless he has local friends, has traded for defenses, or has coupled the tree with another cleverly.
The penalties for specializations and their tradings are inherent in their choices of tech and the compounding difficulty of reaching outside their specialization. This of course depends on the rates set by IDA and I would also note that if development does not leash meta-alliances into localities these specializations could be excessively difficult to enjoy for solo players.