The 49ers need impact players, particularly at two key positions (wide receiver and cornerback). If they're in love with a certain player, they can go get their man, no questions asked. And it won't affect their draft strategy or their ability to move around in the later rounds.
Moving from No. 31 to No. 18 last year only cost the 49ers a third-round pick, and they got their safety of the future in LSU's Eric Reid. They also traded up twice more within the top 100, acquired their "gold-helmet" prospects and still over-drafted a few players.
It's hard to see San Francisco not trading up on Day 1.
Usually, this would be a "no" since the roster is so loaded—and some might peg this as "fiction"—but the 49ers are still looking for help. And again, those impact rookies might come at wide receiver and cornerback—either in the form of a burner or size pass-catcher, or in the form of a route-jumping defensive back that can play the nickel position.
San Francisco has dabbled in rookie backups, but the coaches just don't appear comfortable going that route. They had a rookie backup last year in South Florida's B.J. Daniels, who played as well as anyone could've expected in the preseason, but it didn't stop the 49ers from cutting him loose and going with an inept backup quarterback in Colt McCoy.
McCoy came in with a poor track record, looked terrible in all of his exhibition reps and was still anointed the No. 2 quarterback. This season, Blaine Gabbert will be second-string behind Colin Kaepernick by default, simply because he's seen live action. Experience matters to the 49ers over everything—not to mention that Harbaugh, the quarterback whisperer, believes he can correct some of Gabbert's faults.
The 49ers may draft a quarterback, but if they do, that player will be the No. 3 guy in 2014.
The 49ers will be looking to acquire strong depth and players that can contribute immediately, but they'll also be thinking ahead. Like they did with South Carolina running back Marcus Lattimore, Florida State defensive end Tank Carradine and Alabama defensive tackle Quinton Dial in 2013, general manager Trent Baalke may intentionally draft injured players this year with the intention of red-shirting them.
The Niners don't have room in the starting lineup and have been so overloaded that their practice squad and inactives on game day have become quite the talented bunch.
Like you mention, Clemson guard Brandon Thomas and Oklahoma cornerback Aaron Colvin may be on their radar this year. It would not be the least bit surprising to see them draft one or both on Day 3 of the NFL draft. These are talented players that will likely be able to be had at great value, and they come at positions of need for San Francisco.