It seems an odd way of doing it to me tbh, as I say you're looking at two separate agreements between different parties so I don't see there's anything in it for the selling club, but if they did agree that would be OK. Here though I think Southend announced the fee had been met before there was any negotiation with the player so I think it's incredibly unlikely the contract length had any impact on the fee payment, they're not about to change their conditions based on the subsequent negotiation they're not involved in.
What it does affect is the depreciation of the fee in the accounts. If his contract is recorded as an asset in the accounts at £150k then the depreciation would show as £42.9k per year as a cost over a 3.5 year contract as against £75k if it was over two years, say.
Sorry that's very boring!