I think it should be counted, yes. It's obviously a smokescreen to justify their salary hierarchy. I will always count Neymar's signing-on fee with his salary over the years to see how much he has earned at Barcelona.
I agree completely. While we're at it, though, I remember Rosell saying something about how signing Thiago Silva would be a problem partly because we couldn't fit him into our wage structure fairly... at the same time, there you have Neymar making 15 million a year from FCB only.
Anyways, what I wanted to say was that, if we're taking that fee into account, he's not the second best paid player, he's ahead of Messi. But if we're not taking that into account, I guess Xavi is the second best paid at the moment, before Iniesta signs his extension.