Why was he not allowed to stand for consul in absentia in 50 BC? They had been willing to break tradition for Pompey in more unprecedent ways when he was made sole consul, why not just let Caesar run for consul?
In some ways, the best way to think about the civil war of 49 is less about the constitutional mechanics of the Roman Republic, or even the shifting factions of domestic politics, but to engage in a sort of IR Realist analysis of Pompey and Caesar less as individual politicians, and more as states in their own right.
Notably, Michael Crawford has coined the term "alternative states" to describe the military and administrative apparatus that late Republican dynasts built around themselves, each with their own sets not simply of voters and supporters, but of technocrats, active soldiers, and still able-bodied veterans. These two "alternative states" by the 50s overlapped with the Roman Republic itself, which technically sponsored their armies, and gave them legitimacy through high office and extended commands. But uncomfortably, both alternative states were growing more powerful than the Republic itself, and one might described the 50s as a sort of unsteady triangulation: Caesar and Pompey had united (along with Crassus) to dominate the republic (that non-alternative state!) for much of the 50s, and Caesar had benefited dramatically by strengthening his own position through the conquest of Gaul, which provided him with money, and also a dramatically expanded pool of battle-hardened soldiers. The late 50s saw a retriangulation. Some personal factors no doubt played a role: the death of Julia, Caesar's daughter and Pompey's wife, as well as the slaughter of Crassus, whose presence no doubt helped to balance the alliance. So to, we might see the impact of Roman politics, including the consulships of the Marcelli (brothers Marcus and Gaius in 51-49, and their cousin Gaius in 50), all rabid anti-Caesarians. But from an IR perspective, Caesar's dramatically rising power prompted Pompey himself to re-triangulate, now allying with the Republic against Caesar's ascendant alternative state. Whereas Pompey had previously defended Caesar's command and even laid the groundwork for a campaign in absentia, he now allowed the anti-Caesarian forces to arrange Caesar's recall, and accepted the command of Republican forces. The shifting balance of power, as much as personal connections or constitutional niceties, turned these former allies into deadly enemies.