Without the penalties the cost of IFA would skyrocket to the point that the only way to get a good one would be to slash salary (thus incentivizing tanking) so you would have $40M to compete for the studs. As is, the system puts a premium on planning. Knowing that anything under $2M would be wasted, you could have spent $1.3M more on coaching. While RL comparisons are iffy, the penalty makes sense in mirroring the difficulty MLB teams would have shifting gears in April. In RL, suddenly having an extra $1.3M to spend on, say, scouting, would be of limited value since the 150-200 best scouts would already be under contract for the year. Team doctors and trainers would be set. Most FA would be taken except the odd Stephen Drew. Extra $ available in mid-March would be of limited value.
To answer the original question about why there are such penalties, the problem is similar to what you suggest but in reverse. It would be Payroll going to Prospects, rather than the other way around. You can already budget as much as you want for Payroll. But owners who don't think their teams are competitive in the current season could dump salary (Payroll) and transfer the savings to Prospects to ensure signing an IFA stud. That has multiple negative consequences — 1-Affecting pennant races by giving one or two teams great players at reduced cost (if I'm dumping salary, I don't need to get as much quality back) and 2-Driving up IFA prices, which in turn can lead more owners to dump salary.