You cannot alter the effects of these facilities within the game engine; but it isn't needed either. The resource converter allows you to convert resources already in storage, and so would be used to convert, for example, these organics into minerals. You would extract the organics, and then convert them, virtually increasing the mineral value for your planet (at the expense of organics).
The Value Improvement Plant works as well under finite games; while it adds its value to all planet values in infinite games (going from 150% minerals to 151% for example), it multiplies the *current* value of your planet in finite games. For instance, if you have 1500 minerals left on your planet, using the same facility will multiply these 1500 by 1,01 (making 1515 minerals). So this facility is paramount in finite games, and should be built as soon as possible given how it works.
I do not believe that Proportions is truly designed for playing finite games though (unless the author, PvK, did a lot of work to make the AI work in such games). If you would like to play finite games where the AI can handle its own, the
AI Campaign mod is very likely your best bet. It is based on the Proportions mod, and aims at making the AI a lot tougher (including when playing with finite resources). I will let the author, JLS, to speak for his mod and how it plays with finite resources though.