Turning it On Late

Colleges coaches seem to have no problem with a starter giving them four quality innings. They have seventeen, eighteen pitchers.

Agree with RJM. Also, recruiters/scouts may not stick around long enough to see him touch 90 if he is 83-85 for 5 innings. If you take a closer look at how many pitches option 1 throws in the upper 80's to 90 range compared to option 2, I think option 1 shows more stamina anyway. Just my 2 cents.

It's not unusual for a young  pitcher to run out of gas. That kind of gets corrected as the pitcher moves to the next level and matures.

It's pretty hard to answer as you have left out specifics. 

What were the pitch counts in each inning, did any pitcher go deep into the count and what were they throwing, FB, off speed, breaking ball?

College coaches want pitchers that throw strikes and get hitters out. Good pitching coaches look for players they can help to improve by working on their mechanics. The good ones see flaws they might be able to correct and make them first rounders, Florida's Kevin O'Sullivan is a master at that.

Our younger son typically started HS games at 84/85 but was a few mph faster by the 3rd inning.  If he gave up a run, it was almost always early and as TPM says, he threw strikes and had exceptional command for a HS pitcher.  Thats probably what kept college coaches around for a few innings and allowed them to see the velocity pickup as he settled in.

The college coach who recruited him once told me he was at a game and saw 83/84/85 on the gun.  Was a little concerned but the scouts nearby told him, 'Just wait till the 3rd, he'll be 88/89' and he was.

Stamina is not an issue for recruiter or scouts. A HS body and physical training are typically nothing compared to the next level; in other words stamina can be addressed in the weight room and by natural growth.

(Id also note that velos seen at one game dont necessarily paint a complete picture: exams, papers, baseball work load, a good night's sleep and other daily things all can impact velo. During recruiting, I watched a senior pitcher at a college sit 85. He was supposed ro be low 90s. He had delayed finishing his senior thesis and had been pulling all nighters to catch up. Nine years later, hes still throwing - in the 90s in MLB.)

OP discribed (to me) one pitcher a bit more advanced in that he paced himself. That can be taught.  As TPM pointed out, many coaches look at recruits through  a lense of "what can I improve" with the nascent pitcher - so a non-athletic guy sitting 90 with a smooth effortless delivery may be maxed out; while the 86 pitcher is athletic but has several mechanical issues which can be fixed and therefore has a higher upside.

Both pitchers have potential to pitch D1. Beyond that, its recuiters preferences and perceived ability to fix certain issues which dictate which guy gets attention.

Will scouts/RCs stay and watch an entire game? Depends upon the player, the coach, time available, other  committments, etc. Some scouts and coaches work harder then others; and sometimes multiple kids are playing multiple games on the same day at the same time- and you try to see each one by watching,  e.g., two innings here and three innings there.