To address point 2, projects are budgeted via VDPs in a separate process. For example: VDP-103 [Funding]: Mutation-Specific Codon Suppression for Aging and Longevity - #16 by Shift
Projects that are funded are funded for a set amount. If they need more money for whatever reason, that will be a new VDP. In some cases, they are funded with a milestone-based approach, wher they have to hit the first milestone to get money for the next milestone. So budget overruns are controlled at the level of initial funding.
To address point 3, I think project management will be ongoing since the projects are ongoing. We can revise almost anything via VDPs.