The mining modules gained from those techs could (and should, imho) be moved into the Space Mining techs. It's a logical leap and I find those modules to be more important than the Production-boosting modules. Overall, I generally don't bother with the Production modules unless I have a big cluster of planets (3 or more, preferably with planets which are ideal for Tech or Manufacturing capitals) which could all benefit from them.

As for whether it's intentional... well... the traditional factories are the most expensive maintenance-wise, but, with said Production modules, you can attain some really high-yields. The other methods are cheaper overall, and most do have a other sources for +%Production (heck, the Iconians have a +50% production building they can place on every planet!) which could, overall, make up for the loss of those modules.

Space Mining is for Asteroids.

Perhaps they could spin the resources into their own little tech tree's. Give them names other then "Economic Resource" and "Influence resource" and put in prerequisite techs to build and upgrade starbases. Having a special tech to even build a resource starbase would put an end to the annoying constructor rush for the special resources.