In theory, nothing wrong with that but the old holes had been left exposed leaving an open invitation for water and dust from the road to enter and lay sitting in the spare wheel area. Plugging up a couple of rather large gaping holes with rubber grommets would have tidied the job up nicely.
Most owners I suspect would not bother to be as inquisitive as my mate after similar repair work especially if the outward appearances looked so good.
And punctures are fairly rare these days, so the boot floor is an area that is very much out of sight and out of mind. That is until it comes time to sell and a potential buyer discovers water pooling in the spare wheel recess or a rust-stained tool kit and starts thinking the worst.
There is no doubting the fact that reputable panel beaters and painters are skilled craftsmen who display some amazing talents when repairing motor vehicles after accidents. But a very small pin hole in a repaired body seam or a tiny gap in the sealant used around windscreen apertures can allow rain water to enter a vehicle and, over several months, eventually soak floor carpets.
At times, the leak may only develop when the vehicle is parked a certain way or the rain is from a particular direction, so it's important to check the carpets occasionally after repairs and react quickly to the smell of dampness in the vehicle.
Not a silly idea either to leave a vehicle out in heavy rain after it's back from panel repairs to check for weather-tightness.
If panels, such as doors, boot and bonnet have been repaired or replaced, look for even gaps around apertures and ensure they open and close easily. A vehicle's age will often determine where replacement panels are being sourced from to help keep repair costs down and stop the vehicle from being written off by insurance companies. This is totally acceptable provided they fit correctly and blend in.
Checking for overspray and/or a colour mismatch is another good idea.
If an accident was major and had inflicted severe damage to the chassis and suspension components then ensure the vehicle drives OK after repairs. When travelling straight ahead the steering wheel should be aligned correctly and there should be no obvious drifting to one side of the road when hands are taken off the wheel momentarily.
So assume nothing and do your own simple checks once the vehicle is back in your hands.