I suspected as much, however I've never had an arrangement with my employers to pay my RA directly and the wording of the second part of eFiling popup message is a bit misleading.
Even if they don't pay your RA directly, if they know about your RA they could be including it as a deduction so that they can factor your tax rebate into they amount of PAYE they pay on your behalf. This way you essentially get your RA tax rebate on an ongoing basis instead of waiting for a lump sum at tax return time.
What would you like to know about provident funds? Feel free to ask me anything. I can tell you that unless you work for a company with a provident fund, there's no way you can get one.