1) The Tax Zone is determined from the Employee, and can only be overriden at document level. In a VAT context what really matters is where the expense was made, and not where the employee lives. This means that an employee working in more than one Canadian province would need to file multiple expense receipts. This is a true concern for them as their employees work in multiple provinces. I think that in this particular case, expense receipts (and expense claim line) should have a tax zone field. It can get defaulted from employee, but should still be overridable.
2) There is no way to control the taxable amount of expenses. Assume following scenario: you go to restaurant, and have a 100$ bill + 15% tax. You add 10$ for service (which is always exempt of VAT), giving 125$ total charged to your credit card. The only way to handle that is to split the expense claim in two lines, one that is taxable, and one that is exempt. A simple solution could be to have a "Taxable Amount" field with the expense, however this wouldn't cover every single scenario - in Quebec there's more than one VAT tax applicable, and some products like books are PST exempt but not GST exempt.