Note that, since OCaml 4.01, OCaml marshalling flags include a Compat_32 flag. If set, any marshalling operation involving an integer that cannot be represented on 32-bit OCaml versions will fail at runtime. If you would like to have consistent marshalling behaviour between architectures, enabling it in Coq is probably a good step forward.
(Un-marshalling a 64 bit integer that cannot be represented on 32 from a 32 bit machine always fails. What Compat_32 brings is a failure at marshalling time, from the 64 bit machine.)