BUMP.
Also, the power gains in shards from upgrading (played with Queen Procipinee this time) doesn't update on top of info screen. If I have a an earth shard, and research immortal codex and upgrade it, it should read 2 instead of one according to description (earth power season 1 > +1). Otherwise is hard to tell how much your spells are affected by the shards and their bonuses from the spell book (which doesn't give you an estimate of overall benefits, just states the basic +1 damage per shard or w/e).
I'm not sure what you're getting at here, but I think you misunderstand what upgrading shards does. It only grants you +1 mana per upgrade (and stronger elementals, if you have the Binding trait). Going from an earth altar to an earth temple will not give you more than one earth power for a single shard.
As for the tech tree bug, I have seen it as well with a custom faction that had Binding, but as of .87 was still able to upgrade and receive better summons after the appropriate techs. Haven't tested for .9, however.