The view is that a good father should always put his children first (above his new wife/GF/her kids) and do whatever it takes to maintain a relationship with them. If something is cited as the reason for the child not coming over like this, then the usual advice is that the dad should either see the child elsewhere like a hotel or he should rent/buy another place if possible or his wife goes to stay elsewhere when the child comes over.
The thinking is that this will only carry on till the child is 18 and the dad will have developed a solid relationship with his child in the meantime (without his wife present) so as an adult at 18, s/he won't be influenced by the bitter Ex.
If dad doesn't do that, then he risks the relationship with his child deteriorating, as the child refuses to see him when his wife is around. From the child's perspective, their dad has chosen a woman over them.
I can't agree with this logic at all, on so many different levels.
Firstly, no one is arguing that OP's DH shouldn't have one-on-one time with his son to work through this - just that OP shouldn't be asked to leave her home to accommodate this as it sets a very bad precedent and will lead SS to think that he can get rid of OP on his request.. DH could easily avoid this issue by taking SS for the weekend somewhere rather than asking OP to go away.
Secondly, problems like this don't disappear when a child turns 18. If left to fester, if anything it will become more ingrained and the child has never had to process the fact that their parent has a new partner. You will end up with a situation where the step-parent is always expected to make themselves scarce when the SC is around, and where does it end?? The child won't suddenly become accepting when they grow up.
Thirdly, if the child's perspective is that by even having his partner in the house their dad is 'choosing a woman over them' then that needs to be changed by dad showing them that his partner is NOT competition and doesn't threaten their relationship - not cutting her out when the child's around so they can see they are the centre of his universe. It's not a healthy or realistic view for a child to hold.