1) it was the TEAM'S decision in 2009 to design the stripes that way, NOT Reebok or Nike.
2) per NFL uniform rules, any drastic change in a jersey design cannot be done until 5 seasons have elapsed, so the inaugural season in Santa Clara in 2014 would be the earliest the stripes could be fixed for ALL players (yes one can argue fixing something seemingly trivial as moving the stripes up a few inches should count as a "drastic" change, but I'm not the league and we all know they make a lot of stupid decisions)
3) I think the only reason why Alex, Akers and Tolzien have the full stripes this year is cos they're the only ones who chose to wear Nike's slightly longer cut sleeves that obviously is able to show the full stripes. All other players elected for the less grabby, shorter sleeves which carried over the truncated stripes if the Reebok design.
Seemingly contradictory and doesn't make sense, yes, but in the end it is the team's decision (in conformity with league policy) to continue the truncated stripes (next year hopefully will be the last), and it the individual players' choice if they want to wear the slightly longer sleeved jerseys with full stripes made by Nike (but only 3 chose to).