The only disadvantages are those inherent in the situation.
1. The property owner is around.
2. They know you're on the property.
3. If it's under five years they can have you removed as trespassers; if not criminally at least through an ejectment process.
Well, also it depends on the waiver. Any waiver you sign should be as limited as possible. It should state something to the effect that you will not hold the owner liable for any injury or damages caused by the condition of the property. You should not assume any liability, and you should be careful of other provisions they may include such as inspections, work trade, relinquishing of any rights, etc.
If the waiver is simple then signing it in exchange for keeping your home is the most practical thing one can do.
The next question is what rights does a permissive occupier of a property have. This is a question I have not yet found the answer to.
The owner will likely argue that you merely have an employer-employee relationship such as a property manager. Such relationships are "at will" which means they can be ended without notice at any time.
The former squatter will argue that any work done was in lieu of rent and therefore establishes tenants rights.
One thing is certain though, at the very least the owner will have to evict you as a tenant even if you can't establish tenancy because once you have permission it is not a criminal matter anymore. For this level of extra security alone it is worth signing a waiver.
The only thing that bothers me personally about dealing with property owners who leave their property abandoned is my fundamental resentment of allowing people to let property be wasted while people are homeless. Some absentee landlords have a legitimate excuse, but most are just douchbags. With that said be careful and don't let them take advantage of you.
When the Property Owner Arrives.