With elaborate scripting one could circumvent some of these limitations, but it is hardly a solution.
What I suggest is to make prototypes editable in-game. What I mean by that is:
- Research can change a prototype. For example a recipe for a machine becomes cheaper. A machine has reduced/increased power usage. You can hold more of an item in one stack.
- Researching one technology makes other technologies more expensive or cheaper. For example researching bot carry capacity will increase technology costs for bot movement speed. Researching a 'red' science technology makes other 'red' science technologies more expensive.