I specialise in treating and ideally preventing separation anxiety...
First of all, isolating a social animal, failing to meet that animals need for company, interaction, training and socialisation/habituation is NOT how to prevent separation anxiety, actually it's a really good way of creating a life long separation related problem, or several.
Whether you agreed to a puppy or not, the puppy is now here and if you continue to let this happen you are at best, enabling the neglect/abuse.
Dogs are social animals who evolved to spend time with humans, that is why they are not wolves.
Bring the puppy into the main house, give him beds, soft crates and use gates to control where he goes so he isn't simply running loose round the house unsupervised.
The first step to teaching a puppy to cope with being alone is in fact to NOT leave the puppy alone, but let the puppy be with you, whilst you teach them, via a variety of games and training, to be confident, secure and independent. THEN you gradually build up the time they can be separated from you, and then actually alone.
Confident, secure, happy puppies can be taught practically anything, but puppies who are stressed, distressed, anxious, will really struggle and will be predisposed to struggle with stress later on in life too, so this needs to stop NOW.