Any suggestion of the bike being run with low oil is a potential death sentence and nobody could say what damage might have followed. Before I buy a vehicle, the first thing I check are fluid levels and colors - they say a lot about the owners/dealers attention to servicing. Valves and even tensioner doesn't sound too big a deal, but somebody has to pay for it and work isn't cheap.
Often with mechanical noises you can't be sure of anything or quantify the total repair cost until some dismantling is done. It's not fair to expect a dealer estimate on the unknown and they would rather keep you happy and get the work first, then talk about the 'length of string' afterwards. Sadly it's like clinical cancer investigation. If oil has been a problem then the astute tech will be lifting heads and looking for any tell tale signs.
Because of the uncertainty, I'd pursue any warranty written or implied first. If you bought from a non-BMW dealer, you could get your BMW dealer to give you a written opinion/report covering as many areas of possible problems and some idea of costs. You may have to pay for this and offset it later against any claim. If you have any sales warranty, argue it on reports and estimates, not standing by the bike arguing if something is noisy or not. If you can trace any previous owners, you may be able to persuade them to fill in gaps or history your dealer tech. would never find.
Since bazra mentioned lower bearings, you should find out if the noise you get comes only when the motor is under load (high gear low speed) - that's likely bad news on lower bearings. If there's a problem with lower bearings the oil pressure often goes down, but on an investigation I'd put this near the top for techs to check first. If your noise comes for power on then goes on throttle rolloff, then timing chain/valves.
No doubt you are hearing all this with the plastic on. I think I'd take off the sides and try riding the bike with a skull helmet so I could hear the noises properly. It's too soon to get downhearted, you could be lucky, have a fairly minor problem and still end up with a good bike. Good luck.
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