I use multi-stage engines (inspired by the tilting wingtip engines on the "Serenity" from Firefly) which transition from fanjets to turbofans to ramjets to scramjects to fusion to antimatter-boosted fusion as the ship travels from surface out to jump point. In the process, these engines consume ~2% of beginning ship volume in fuel (plain water), since they don't need to burn onboard fuel until they transition through the upper reaches of an atmosphere and on into vacuum. I chose plain water because although it is less efficient as a fuel, it is *much* less dangerous to carry aboard, requires nothing in the way of special equipment/tolerances to store and has other potential uses (such as providing emergency replacement oxygen for life support).

 

For me, all contragrav can do is cancel gravity. The only limit on the volume/mass supported is how many credits you want to spend. Designers of commercial vessels IMTU don't want to spend a whole lot, because interstellar cargoes are usually of comparatively low mass. E.g. mine is a Small Ship Universe, in the main. In order to get thrust, vehicles of all sizes need reaction engines.

  

IIRC, the main reasons Drake uses harbors as downports are:

1) The relatively rudimentary autopilots available in his universe mean that landings much usually be done manually. A manual landing on water is much easier than on land, since in the final seconds prior to a touchdown on land your vessel is subjected to thrust reflected back from the hard surface. Without automated feedback adjustment available, this reflected thrust can cause less skilled pilots to lose control, resulting in broken ships. Landing in water avoids the issue of reflected thrust entirely.

2) A lot of the worlds in the RCN universe are just barely at Fusion Tech Level, if not below it (sometimes far below it). Their bigger cities are therefore usually already centered centered around harbors. This makes putting a downport on the outskirts of the existing harbor facilities quite practical.

3) Using onboard high-speed pumps, starships can quickly self-fuel themselves from the water in the harbor, thus avoiding the need to rely on (possibily hostile or greedy) port officialdom.

4) Even dialed down for in-atmosphere use, the exhaust from the ship's thrusters is hot enough that - were they touch down on land - the surface surrounding the ship would be heated/irradiated enough that a crew would have to wait some hours before being able to safely exit their ship. Even if wearing hard suits, a crew would need to wait several minutes to avoid overheating the suits boots during the trip out beyond the heat-blasted space . . . and wearing these might make the locals think they were being invaded/raided (with predictable results). 

IMTU - since my multi-function engines aren't pure fusion rockets - my lower-class downports are usually concrete hardstands along the banks of a body of fresh water, from which ships refuel using their own hoses and pumps.