**In this sense, yes this is justified. Also, the differentiable structure is a background structure in the classical case (topology is more subtle). We start with a manifold and pick one of the infinitely many differentiable structures.**
Also topology is important since it can have curvature ramifications - the Gromov - Bishop theorems and so on...
**
BI isn't a rigorous statement. **
We are getting somewhere.
**
Kretschmars objection is of course silly, one can write any theory in a more general way if one breaks down the generality of the language by introducing distinguished elements (non rotational invariant systems can be written as rotationally invariant + a distinguished vector for example). **
It is not that simple, for example I can dynamically pick out a preferred coordinate system and thereby *appearantly* violating general covariance (see K. Kuchar work on quantisation in the gaussian gauge). I can write down a fully covariant action pricinciple which gives me Minkowski as a preferred background. On the other hand, I can write down GR as a gauge theory on Minkowski space time (see the work of Dorian, Hestenes and company), without having to worry about general covariance at all.
**I agree we need to implement the constraint algebra (or the part of it responsible for rendering a certain structure kinematical). Most of it is implements, the gauge and 3Diffeo constraints in particular. **
Well, also here you need to be careful, it is not so that the diffeomorphism *algebra* is implemented (your algebra does not exist due to the lack of weak continuity). So, it seems a very difficult task to be able to speak about a suitable interpretation of *spacetime* covariance (with the correct classical limit) here.
**
And yes, the construction and interpretation of R/D involves kinematics, but only to supply interpretations, the resulting Observables are invariant under the full constraint algebra. **
Ok, but that is at the *classical* level no big deal at all. Moreover, a hardcore relativist would expect local observables to be defined without kinematical background structure (and at the quantum level you have troubles with your Hamiltonian constraint) - so again you use a rather personal interpretation of BI here.
**
If there is nothing in your universe but the BI theory of the one field, then this localisation is of course of questionable physical validity. Luckily that's not the case. **
Well, I am not sure what you mean here but in *any* case you need to make such identifications. If you include matter you have to color particle 1 red, particle 2 blue, particle 3 yellow and so on - so you will have many red spots in each universe and depending upon the questions you ask your ``consciousness´´

will be in different superpositions of universes - sorry I like to state this in a path integral language, it makes everything more ``visual´´. Now, you might say: well that works apart form the tiny facts that your number of orthogonal states blow up super exponentially and the small issue that you do not have properly understood the quantum constraint algebra yet. Moreover, in this way, you cannot setup a unification between matter and geometry (so again, this is not necessarily a virtue). In case you would be interested in such enterprise different point identifications will lead to different physics (different ``states´´ if you want to). In that case, it seems much more intelligent to start out from an interacting matter theory on Minkowski and to deduce your metric as an effective variable as EINSTEIN himself suggested (you see everyone uses some words of the old master in different ways and ignores with the same ease other equally important ideas

). I mean, good old Albert was never able to explain the measure stick (idealized and put on the tangent space), a theory of measurement physically originates from matter interactions and is weakly temperature dependent (in the old days they just counted the number of atoms in a stick, noted down the temperature, and used that as a reference). Really, even if this is not going to change anything for you, it is good to know of the difficulties (again with EM say) the view of the measurestick as fundamental variable carries in itself.
Cheers,
Careful