Not really that complicated, is it? By increasing the effective price of the player they decrease the chance of it being bought. There's also the elusive (and probably not that important to them) issue of
more tax income to their region .
Making it has hard as possible for an unwanted deal to proceed is pretty self-explanatory. Even if they are aware that they won't be able to prevent the transfer it's logical that they will make it as hard as possible to the buyer. It also makes less likely that buying clubs want to go through this hassle very often, thus limiting the appeal of their players.