This offense was at its best the first 6 or so games prior to his calf injury when he was running RPO, and using his legs more often. He didn't wait or was hesitant to run as he is now. He needs to open it up again and put pressure on the niners' defense by showing he will run it too.
Not sure what you were watching in September and October, but he was functioning pretty much as a pure pocket passer in the first 6 weeks of the season when the offense was so on fire. Dak had 22 rushes in the first 6 games, about 3 per game (3.66 to be exact). That's what you call "using his legs" a bunch and "opening it up" to put pressure on the defense as a running QB? 3 and a half rushes per game?
For reference, Tom Brady and Drew Bledsoe averaged 2.08 and 1.99 rushes per game over the life of their careers. Vinny Testaverde averaged 2 per game. Troy Aikman averaged 1.98 rushes per game. That's basically the baseline for what an absolutely immobile statue of a QB can be expected to do, is average 2 rushes per game. (For what it's worth, rushes per game isn't a metric of athleticism. Tony Romo averaged fewer rushes per game than Brady and Bledsoe and Aikman. But we all know first-hand from watching his entire career that he was quite athletic and moved around quite well. Romo could scramble much more deftly than Troy or Bledsoe, yet he averaged fewer rushes per gam than either of them. He tended to use his mobility to escape the rush while still remaining in the backfield and keeping his eyes upfield, intending to salvage the play with a pass instead of with a run.)
What do actual running QBs do when it comes to rushes per game? Well, Josh Allen averages about 7 rushes per game in his career. Tyrod Taylor averages about 7 per start also in his career. Vick rushed 7.5 times per start. Lamar Jackson and Jalen Hurts rush about 10 times per game. That's what actual running QB's rushing output looks like. Statistically, Dak has never actually been a running QB. Never even sniffed that kind of rushes-per-game output, even in his one extreme outlier season (when his rush attempts per game stat ballooned by 1 rush per game, likely a result of him running for his life more often as his o-line's pass protection declined). He's more mobile than a statue, sure, but he's never been a full-on running QB.
But back to this year and the claim that Dak was using his legs and opening it up a bunch more earlier in the year. In the first 6 games this year, Dak ran 22 times. But a full 5 of those were kneel-downs, so that obviously deflates the number from 3.6 rushes per game to 2.8 per game.
It is true that his rushes per game dropped off in the 10 games since the calf injury. But I'm not sure how much that has to do with his injury or his willingness to run. Realistically, I think the drop in runs can almost entirely be accounted for by the reduction in kneel-down duties during that stretch.
The team went 6-4 in those 10 games, so right away that's 4 losses where we couldn't possibly have knelt down at the end of games. And of the 6 wins, 3 of them were massive blowouts that led to Cooper Rush swooping in to mop things up and handle the kneel-downs. Cooper Rush has 9 rushing attempts this year, and 8 of them are kneel-downs that came during our blowout wins in the 2nd half of the season.
If you added those 8 kneel-downs to Dak's rushing total since his return from the calf injury, then his rushes per game average would be 3.4 (only a hair lower than the 3.6 average he had earlier in the year or the 3.6 average he has in his career).
It's really just the fluke of him not getting kneel-downs that made his rushing attempt numbers look like they took a tumble.