RajKumar,
one of your issues is that you refer to this as a "pipeline", but then quote a piping code (B 31.3). B 31.3 doesn't do buried piping very well and you need to make sure that the "pipeline" is actually piggable, otherwise you are in trouble.
IMHO, testing of pipelines should occur with the pipeline in its "as installed" condition, i.e. laid in trench, backfilled (maybe not final re-instatement) and all connections and below ground / above ground connections made.
Testing in fuel systems is normal and just requires that you clear out the water using pigs initially then perhaps either a swabbing run with a MEG or similar, vacuum dry or just accept that the first few cubic metres will have some water in it. what you need to do varies with each system.
My motto: Learn something new every day
Also: There's usually a good reason why everyone does it that way