It seems like Aiyuk's agent did him a disservice in failing to convince him that disputing the voided guarantees was the right/smart thing to do. But maybe he tried and Aiyuk was stupidly adamant, who knows.
As far as the current situation and how it impacts Peters' ability to sign Aiyuk as a FA, further digging indicates that Aiyuk's status defaulted to being on the roster as of the beginning of the new league year, and it appears (not positive about this) the first date on which SF can renew the 'reserve/left team' designation is the day after the final roster cuts to 53, end of August - which lines up with the roster bonus of $9.6M due beginning of September and which I can't imagine SF wants to pay. Before that, SF can save $6M against the cap if they release Aiyuk by June 1.
So right now, it does appear Aiyuk is taking up a roster spot (but only one of 90) and counting against the salary cap for $14.6M, and you'd think the worst case for FA signing purposes would be SF releasing him at the end of August to avoid the roster bonus. That would be extremely unhelpful for the Commanders, who'd already have their own camp completed and roster set for the upcoming first regular season game. No way Peters can logically including Aiyuk in any forecasted WR depth chart, way too speculative not even considering unknown condition of his knee.
This all helps explain why Peters did apparently take swings at Pierce/Doubs/others so far in FA, but it also makes it more disappointing we haven't done more at the position other than sign slight upgrades to the off-the-street type guys we signed both early (Gallup/etc) and late (Chosen/Moore/etc) last year.