Focussing ONLY on the financial differences.
A 50% scholarship at a school like Vandy (top tier academic private school) is worth roughly 30k per year. It is not taxed. So a family needs to come up with an additional 30k per year. (Note this also: make sure the 50% includes room and board; many times the percentage the coach offers is bases ONLY on the tuition part of the equation.) To satisfy the family contribution of 30k, requires roughly 45k of pre tax w-2 earnings. Assuming no inflation for the entire four year enrollment period means a family will need 180k in pretax earnings to get the player a degree and into proball after graduation (no meaningful bonus).
With the player signed after HS and pocketing all the remnant of his 400k bonus (let's say 200k), the player also has the MLB scholarship in hand. One original OP assumption was that the player would be released after four years. That assumption is not based in the facts known when the contract was signed. The original HS draft contract binds the player for six years. The only fair assumption is that the player plays his full six years and his career is then over by mutual decision (remember the player cannot just walk away early without (a) losing the MLB scholarship and (b) repaying (with after tax money) a prorated portion of the bonus).
Over the six year playing career, part of the bonus was assumed to be used every year. I think 25k per year was a bit much; but we'll use OPs original figure of supplemental support of 25k per year. Because the bonus money was needed, there was no possibility to invest that money safely and still protect the principal; therefore any interest earned on the balance was minuscule in the present interest rate environment. Once the player's six year career concluded his bonus money has been whittled down to a bit over 50k. (I think within the 25k per year supplemental support would be the vehicle purchased with the bonus money.)
To recap, the player now has 50k in the bank, his career is over, and he has the MLB scholarship, and he's 24 (we'll assume no obstacles to actually attending school like wife, kids, lack of desire).
Costs of attending a school like Vandy have now gone up 30% (5% a year for six years, ignoring compounding) and now cost roughly 75k per year (excuse me, I just passed out). So player (no longer a kid) needs to come up with 300k in cash to pay for four years.
MLB pays as follows: 60k per year taxable; but the amount requires that the player live in the cheapest way possible so he is living in a freshman dorm and eating on the meal plan (don't know where wife and kid will live, but he'll figure that out). If he wants to live in a more age appropriate environment, MLB will not pay for that. The 60k per year shrinks to roughly 40k after taxes. So, of the 300k cash needed, player has 210k (160 from MLB + 50k in bank), leaving him 90k in AFTER TAX dollars short (Let's say 140k in taxable w-2 wages.)
Comparing apples to apples by result: both players careers are over and both have degrees from Vandy. HS draftee needs 140k in taxable w-2 wages and has no bonus money left. College kid needs 180k in taxable w-2 wages to get there. The HS kids advantage is 40k in taxable money.
i didn't run the calculations with a state school with a 30k price tag. First, in my state this will probably just barely cover the costs today - certainly not in six years. Second, (and I'm a state university grad), there is a difference to some employers between a degree from Vandy and a degree from UT. But the economics are similar - the difference in purely finances are pretty small with a slight purely financial favor to the HS kid.
As we move further through the years, variables which we're keeping constant (and therefore ignoring for these calculations) make the results really suspect (e.g., will the player stay at 50% scholarship or transfer after year one of no playing time, will the costs really not increase over four years, will the player get drafted after three years, did the player actually stay on track to graduate after four years, does the HS kid have the motivation and skill to complete college, etc, etc.) I would say that based upon the OPs assumptions (with the minor change of the length of the HS player's career), the difference in economics is not a huge difference.
If the economics for a 400k bonus is not really a determinative factor, we're back to the intangibles which push one way or the other.