Things to consider:
1-If you can't afford the software required, then you could sell the hardware(which has decent value) and replace with hardware that will work with PT Vanilla.
2-If you're going to use any other DAW, then HD/Native would not be a good choice at all.
3-you mentioned the native PCIe card or Thunderbolt, but you didn't mention what interface you would be using with it(the card or Thunderbolt box are useless without a connected Digilink device).
4-If you are trying to put together a working setup, maybe if you describe your needs in complete detail, someone will have some good recommendations
