Sir , I would like to give answer to your queries point wise 1) yes all milk teeth finally falls off. But the last tooth that falls is at the age of approx 12-13 years. Each and every milk tooth has its role to play till they fall. First they help in eating and phonetics then at the age of approx 6.5 - 7 years when permanent molar erupts there role changes to space maintenance for the permanent teeth which are beneath them and chewing.if we remove milk teeth early there are chances of permanent teeth not erupting at there usual place . 2) yes they can harm in some cases to the permanent tooth beneath them as infection can spread to the underneath tooth. 3) permanent 1st  molars erupts at the age of6.5-7 years and no deciduous teeth falls, they erupt posterior to deciduous(milk) teeth and most of the time there is misconception that these are also deciduous as none of the milk tooth has come out yet .

Every milk teeth is replaced by a permanent tooth..caries in decidous tooth wouldnt affect the permanent tooth

Milk teeth having deep caries usually fails to fall of on it's own and may cause deformation in permanent tooth or causes problem in eruption . If all the teeth have been treated then it won't cause any problem in eruption or health of permanent teeth. RCT filling material used in milk teeth dissoves by itself unlike in permanent tooth. So no worries. Just make sure to take proper care of your child's oral health.