Is it fair for my employer to pay managers the same amount, one being on EP, BUT tops up CPF for the local and consider it as not part of the paydeal??

Yeah I think this is seen to be quite common practice in most companies in Singapore? i.e between locals and foreigners it looks something like this for a same level manager.

For a Local:

• Gross: $3k
• Take home: $2.4k
• CPF Employee + Employer: $600 + $510 = $1,110
  Total = $3,510

For a foreigner:

• Gross: $3,510

Because they factor in that amount with the (20% + 17%) of gross salary which is quite a huge sum actually.

Well, essentially the cost to the company is the same. Yes, as locals our take home will definitely be lesser but at least it earns a decent interest and if you use CPF to pay for your house, doesn't it come back to the same thing.