Even if that is the case, so what? It has no bearing on whether upgrading is ethical. If a company requires all of its employees to only buy Economy, with no incentive, it's not unethical for the employee to upgrade using his/her own resources. If the company merely suggests it and offers an incentive, then again, as long as the passenger buys the lowest fare possible to meet the terms and/or spirit of the TSP, it's still not unethical.

I would argue that if the company discouraged those who bought Economy under the TSP from upgrading, fewer people would do it than if the company said nothing or even encouraged people to upgrade... people are more likely to buy Y, incentive or not, if they think they can upgrade should they choose to. Therefore, if the company actually does intend on eventually instituting a "buy Y only" program, it should not prevent employees from upgrading using their own resources.

In the U.S., FF points are not taxable if they are accrued through a purchase, even if that purchase is made by someone other than the person accruing the points. Or, rather, even if they would be taxable, they are not taxed. The only time FF points are taxed is when they are "earned" without an accompanying purchase, e.g. through a sweepstakes. Money earned under the TSP would be taxable as income; FF points are not.