Yes, it's all coincidence that Varys -- who's so intent on destabilizing the realm that he later kills two men that appear to be competent at ruling it, and also knows Shae is with Tywin -- gives step by step instructions to Tyrion on how to get through the tunnels, informs him that there are weapons in the room, and there just happens to be a way for a midget to reach the crossbow.
No way to prove it either way, but this seems like classic GRRM to me.
1) Jaime forced Varys at swordpoint to free Tyrion. Jaime discussed his plans with no one. So, unless Varys was prescient, there is no way he would've known to place a chest there *before* Jaime got to him.
2) There is no way for Varys to know who would be in the room when Tyrion was released - or where they would be. If Varys wanted to arm Tyrion
it would have made way more sense to give him something *before* having him enter the room (perhaps even following him up and giving him a weapon before he goes in).
3) There is no way for Varys to know that Tyrion would even recognize where he was. It wasn't like Tyrion had been in the secret tunnels before.