I'm not very familiar with these rules, but you're definitely right that there are some complications. I have a friend who works for CRA and commented that he would never claim costs of a home office in a residence he owned, simply because the tax savings wouldn't be enough to make up for the headaches and tax audits which would result. (Claiming a home office in an apartment you're renting is much easier, since there's no capital gains to worry about and there's an easy paper trail for how much the space costs.)