Bosa is playing a dangerous game - threatening to hold out for the year will ultimately hurt him more than the Chargers. He won't be a top 3 pick next year. In all likelihood he'll drop several rounds. Even dropping to the end of round 1 will significantly impact the bonus money and weaken his position about off-set language since the further you drop the more rock solid standard that becomes.
On one hand I understand the financial argument he's making. He wants his money now so he can invest it now and get the benefit of it rather than having the Chargers sit on it and do the same. On the other hand, if he really does sit out the year he's not getting that year of earnings back ever and that giant bonus is gone until contract number 2. Even if he stays in the first round he'll risk losing huge money. The difference between the 3rd slot and the 32nd slot is about 18M dollars in total value. I'm sure the Chargers realize this which is why they aren't choosing to capitulate. In the end, Bosa will lose much more than San Diego if he does, in fact, refuse to play for the whole year and re-enter the draft.
Since Bosa can't force San Diego to trade his rights, if I were San Diego I'd make it abundantly clear that he will not be traded before next year's draft. His current draft slot will be allowed to expire and he will be re-slotted when he is re-drafted. If he were to sign next March, even if his rights were traded, he's still technically the #3 pick in 2016 and entitled to that slot until the 2017 draft starts.