and to answer my own question:
When setting a boundary, I think you need to balance the comfort you give up for yourself with the freedom you take away for the other. Very important is that these things should be valued by the persons to whom they apply. E.g. when setting a boundary for my partner, I should be the one that values the comfort I have to give up, but my partner should be the one to value the freedom that she has to give up. Only after communicating very clearly can you ensure these are balanced.
As long as there is balance, the boundary is ethical. When I try to take away too much freedom, or when I have to give up too much comfort, one of the partners gets an unfair deal.
(Since this answer is not working for the relationship I'm in, I'd like to hear others, so I can learn something.)