I tried to attack with eels squad but Silas got himself killed just a few times too many, so I reloaded and decided to weaken scrappers before main attack happens. Seems easy enough, waste a few gangers and fall back to the docks...But then I thought why not kill them all by my self since I play on classic and get all the xp, also because I usually try to end all combat encounters without allowing any foe firing a single shot or using meds (for extra challenge and loot). That was a bit long but after a few hours, I found the right combination and Depot B was devoid of life. Then I go to Silas and start the "attack"...now I did not really expect that there would be anything different because games usually tend not to cover every option but seeing the eels and sgs soldiers just stroll through absolutely dead compound and then act like they were part of the skirmish when I did all the work solo was sure disappointing and immersion breaking (because game did not recognise unexpected approach).
It is possible that I am mistaken and there is acknowledgement of that choice maybe if you attack the base before striking the deal with eels I did not try it out. Yet I strongly believe that there should be a special option and extra content when you proceed the questline. When Silas asks you to plant the bomb in the caverns there should option to convince him that if all he wants is to take the scrapper HQ he can just ask and you will "get it done". Naturally, even though Silas sees you as a capable individual he will still see your "plan" as absolutely derailed so you'll have to convince him. Both persuasion and intimidation should be possible. Needless to say, there should be an option to forfeit this suicide mission and agree to original plan (Silas will be annoyed) but if you actually manage to pull this off he should be very impressed and throw some extra cash (because you got him what he wanted without risking any of his men or actually damaging the depot with explosive diversion).