I can't see it coming in on time and on budget either. However, we should remember a few things:
A project likes this must incur significant upfront costs for route selection and design before a spade ever gets in the ground.
As with all construction projects, changes costs money. The row over Charlemont, for example, means returning to the drawing board and incurring redesign costs. The 2023 figure, I think, included MetroNorth costs - which has since been dropped. Many of these changes are driven by politicians responding to their constituents - this is a feature of the political and planning system we have rather than one specific administration. I expect there'll be more tinkering before it gets going ... regardless of who's in government at the time.
If you want a project like this to have any chance of coming in on time and budget, then a good design phase is essential to produce a properly specified and costed plan, followed by having the discipline not to make changes as you go through construction. Ands of course, even with both of these, there's likely to be cost increases. There's often good reasons why you need to change your plans as you go along - not to mention increases that may arise on the cost of labour and materials.