Projected as high as No. 1, he went to Pittsburgh with the eighth overall pick, failed to sign and returned to Stanford for his senior season in 2013. He's not concerned about the difference in a couple of million dollars at this stage, or delaying his possible path to the big leagues by a year.
Appel was the only unsigned player among 31 first-round picks last year, turning down the Pirates' $3.8 million offer in the first year of new restrictions designed to slow draft spending.
He hopes to pitch Stanford to the College World Series and is set to finish his degree next month in management, science and engineering.
Appel isn't about to say that he might have been selected No. 1 had he not been represented by Boras, and he said he never considered switching agents.
"I've never thought about that," he maintained Friday. "I don't think any team is unwilling to negotiate with Scott Boras. As my adviser, I understand that he does a really good job for his players. I trust in his abilities. We have a relationship where we're honest with each other. I can't tell you what the teams were thinking because we never talked to any teams. Whether teams made assumptions that weren't true or whatever it may be, obviously we saw what the result was. What happened happened. We just kind of have to go from there and make the best decision possible.
"At that situation, the best decision possible for me was to come back to Stanford. I honestly believe that in the bottom of my heart, for a number of reasons."
Appel was 10-2 with a 2.56 ERA in 16 starts for Stanford last season, with 130 strikeouts in 123 innings, raising his college record to 18-10.
Like No. 1 NFL draft pick Andrew Luck—a more high-profile Stanford star now with the Indianapolis Colts—Appel chose to stick around campus for his final year. The top factor was finishing his degree, something to fall back on after baseball.
"We're very fortunate we have Mark Appel back for his senior year," Cardinal coach Mark Marquess said Thursday during Bay Area college media day. "We weren't counting on that. He's been so darn consistent and gives us a chance to win. That won't change."
Even if Appel drops below the top three picks in June's draft, he said won't look at his decision as a mistake—"Not at all, definitely not, no."
For college baseball, Appel has become the positive example.
"Hopefully it gives an opportunity to really make college baseball better," San Francisco coach Nino Giarratano said. "It's really tough in college baseball to lose kids as juniors, but it's the dynamic of the sport."
Under the labor contract agreed to in November 2011, each team has a total pool of money from which to sign players without incurring a tax. That number comes from the sum of set figures—$7.2 million last year for the No. 1 pick, $6.2 million for No. 2, $5.2 million for the third pick, $4.2 million for No. 4, and so on. The 50th overall choice, for example, was slotted for a $1 million bonus, while it was $500,000 for No. 95. Picks 300 through the end of the 10th round of the draft were pegged at $125,000 each. Teams and players could negotiate the amount of each deal.
If a player didn't sign, the team lost that slot's amount from of its pool. And if a player signed for less than slot, the difference could be shifted to contracts for other picks.
"It definitely changed the dynamic," Appel said. "Who knows what's going to happen as far as the CBA, the draft in the future? Maybe this will play a part in it, maybe it won't and it will have no effect. It was just unfortunate to see teams that have millions and billions of dollars trying to take advantage a little bit of some of the college players, some of the high school players. This definitely would not have happened in last year's (2011) draft. I'm not making excuses or upset about it. It's just different. Last year was a very rare situation what happened."
Appel said he can't put a percentage on how much the money factored into his decision. But clearly, there's a big difference between $7.2 million and $3.8 million.
The amounts for this year's slots will be announced in April. He realizes some people will have their mind made up about him already and assume he is greedy.
"I can't control that. ... It's not all about money for me. There are a lot of things I value more than money," Appel said. "It's unfortunate that the only thing that fluctuates is the money. That's the only variable, if you were to make an equation of the value of Stanford and value of signing. The only thing that changes is money, and if the money increases, the value of signing obviously increases. We just saw at that value the value of Stanford was greater than the value of signing."
Appel is confident his work this winter and spring at Stanford will still prepare him as well as if he were headed for spring training next week and gearing up to pitch in the minor leagues this season.
"If you go into the more business side of things and baseball side of things, I'm still young," he explained. "Everybody said, 'If you don't sign, you're pushing your major league career back a year.' I don't see it that way. I don't understand how people can say that I can't keep working and keep getting better at Stanford. It might be a different situation and scenario than a minor league team, but I still have the opportunities to improve my game, get better, to just grow as a baseball player and a teammate and prepare myself for the next level."
Appel received advice not just from Boras but also his parents and a number of people in his close circle. If he is unpopular in Pittsburgh, that's OK.
"If they're going to boo me, then so be it," he said. "I'd love to sit down and have a meal with them after the game."