I need to be able to change things like the TCP scaling window and timestamp in the firewall, but I can't find any way to. Linux already has these features available, so what gives?

Linux used only as firewall for do that or Linux used as Desktop OS?
Actually non-beta version do not have those settings, but I think neither beta have it...

as firewall or as Desktop OS?

Both

interesting functions,
we would also have to add change the destination or source IP of the packet (and recalculate the "CRC")
without passing it through NAT or similar ...

Or in synthesis, give the ability to change every single aspect of the packet.

give the ability to change every single aspect of the packet.

This is what I would love from RouterOS.

I hope in future, when the routing part of v7 is done, someone start to work for do this....