My answer would be yes it is completely consistent, modulo the caveats found in MTW chapter 18 or in Weinbergs book. Starting from linearized gravity, you have to bootstrap your way up to the full nonlinear equations, but that works fine and there is no problem with causality.
There is a small technical issue for global nontrivial topologies which means in practise that you have to be careful and glue together several coordinate charts, but again that has been done and there isn't much of a problem.
The bigger problem is what if you want the local chart to be something other than a connected Euclidean topology. We know of no physical example where that would not be the case, but if you insist on being completely general (perhaps more general than nature herself) then you would have a case.
Anyway, more generally there are other perfectly valid formulations of GR other than 'pure' linearized gravity, where you do need to break the diffeomorphism group and specify coordinates from the onset. For instance, everytime you use a vielbien you are explicitly providing a background dependent picture of GR (in terms of frame fields)