I can promise you, in the eyes of the coaches using all four downs comes somewhere around Cougartails are an inch smaller in terms of concerns.
I have never once been involved in a post game or film session conversation where one of the coaches said, "Man, we had to use all 4 downs against this over matched team three times to score" and if anyone had said that we would have laughed at them.
This was the #4 defense in FCS last year, they forced BYU to punt twice and gave up over 500 yards to us, so no, there is no cause for alarm because BYU needed all four downs twice, that's Football, regardless of the opponent. What would have been concerning is going 0 for 4 in 4th down situations, because that would mean the plays you have carved out for that situation are lacking.
The priorities BYU is working on in no particular order from that game are/should be:
1, 2 and 3 - Getting special teams cleaned up, this phase of the game is THE most important and wins or loses games. We can't can't have the lackluster play in this area we had Saturday throughout the season, or it will cost us 1 or 2 games.
4-Containing mobile QB's better, giving up long scrambles is a deflator for a defense, especially in second/third and long. Whether you do it through rush lane integrity/contain or utilizing a spy, this is something BYU coaches are addressing.
5-Consistency in the run game. The run game was much improved, but there were for sure some gaps in communication or missed blocks. Keim and Makasini are two that will get called out on this in position meetings.
6-Dropped passes and more equal distribution. This receiver room is too talented and the drops Saturday are unacceptable. Now receivers also bailed Retzlaff out a couple of times, so credit there, but there needs to be consistency and the coaches/QB need to get ball distribution fixed, whether that be through tweaking route execution or working progressions more. Lassiter should never put up a 0 in receptions and Roberts does not need to be the main target every game. Of course this is one small sample size, but I would be having conversations about this, utilizing all the talent.
92 - Cougartails appear to be an inch shorter than last year
93-We needed all four downs 3 times Saturday.
For perspective, 11 Big 12 teams played FCS opponents this week. Only two of those schools punted less than our 2 against SIU (Utah 1 and Kansas 2) and both of those schools also went for it multiple times on 4th down (Kansas 3 and Utah 4) and I promise nobody on their staffs are concerned either.
It's good that this is one of your main concerns, it just shouldn't be and I say that respectfully.