They can't hire experts to decide where to put the cash. Anyone who can truly know where to best put cash will become or be hired by a VC fund and make orders of magnitude more money than they'd be paid by the EU.
Ie. "we will pay you to work for 3 saturdays to investigate these 5 companies and stack rank them on the question of 'contribution to increasing EU semiconductor exports between 2023 and 2030'".
I know I'll sound kinda defeatist, but I just don't think it's possible to reliably setup a bureaucracy that's competent in funding innovative research. The incentives are just not aligned.
If you are truly investing in innovative companies. You'll inevitably spend taxpayer money on truly stupid stuff. The first time a major newspaper reports something like: "10 Million Euros spent on using bath sponges to desalinate water while people are living in the streets!" it's game over. The agency will be permanently risk averse.