No, not likely to be making money on this. The costs there are the actual costs.
I've gone through clearance several times and it's costly and timely. I've cleared each time and secured the work I was going for.
Key question though has to be the "we can't guarantee you a job" bit. I think you need to go back to the employer / agency and say something like:
"I am happy to pay these costs on the premise that it leads to work. If it comes back negative and I don't get the job for that reason then I understand and I'll pay the costs. If it comes back positive and I don't get the job then you have to pay the costs (within 28 days)".
I'd want a contract to that affect. It takes ten minutes for an employer to draw something up like this.
That to me sounds very fair but I am an IT contractor and happy to pay for checks in order to win work. If you are a perm then you are absolutely in your right to say "You are paying. If you want your staff checked, you are paying.". In practice, it depends on what you do and the job you are going for. It's not a case of one size fits all.
Final note: we should keep in mind some clearance procedures can be done by the employer, some can't (such as Disclosure Scotland). Most employers / clients simply say that you must provide evidence (the certificate) of clearance if they are not able to do the checks.