As far as HEC-RAS calculations go, the software takes your cross-section Manning's values and your downstream reach lengths which approximate a 3-dimensional model and squish them down to a point-value for energy loss along the long section of the creek; for the purposes of calculation, you have a 1-dimensional model, so switching your LOB and ROB won't make any difference.
If you maintain convention with regards to your x-section stationing, you will be much better off when you, the reviewer, or any other engineer revisits the model; particularly if you add to the model at a later stage. It might also save you some extreme confusion while trying to do your bridge contraction and expansion calculations.
Theoretically if you document your break from convention in your model development report, you are okay... but who reads the model development report when there are fun HEC-RAS files to dig straight into?
Please note that the latest version of HEC-RAS is 3.1.3, not 3.3, and similarly, previous version 3.1.2, not 3.2!