As I see it, there are two advantages of an atmospheric grade spacecraft over a void grade craft.
Granted, Lander-grade craft also have these advantages, but there are plenty of reasons to design a ship so that it cant land. The first, best reason is cost its just cheaper to build a ship that way. Second is a function of design. Especially for larger warships, landing a ship of that size would require additional bracing design for sitting in a gravity well, enormous landing gear (and associated operating cost increases for tires or whatever), etc.
Another reason for warships to be designed so that they cant land is weaponry. The larger the ship, the more problem it will have with "blind spots" places where it cant "see" or shoot. Spacing sensors and weaponry around the ship in all directions solve this problem, or at least partially solve it. Of course, this means that designing such a ship to land has added costs and design problems associated with it.
And of course, some ships are just TOO big to land, period.
Now, anti-gravity technology such as that found on flitters can help solve this, but large ships, or ships that need to dedicate more of their power to things like weapons and shields, wont be as likely to use such features, even if the technology is available to the builder.
Which is why I think that the two frigate examples in FL:T should really be considered atmospheric grade, rather than lander grade. True, this is a preference thing, but those ships really are large enough that they should have a lot of trouble landing. Both have significant amounts of weaponry and large shields enough to make anti-grav landing improbable, as it would drain too much power. The range of weaponry and size of the ships mean that it should really have turrets spaced around the hull to cover various sectors. And, although artwork isnt the best argument, the illustrations of these craft indicate a non-landing ship (and maybe even a non-atmospheric one, but ).
A related problem is the rating of the Runt Shuttle and Republic Dropship speeds. Both are listed as having speeds in the "mach" category. Now, this is appropriate in one sense for a craft that is intended to operate in an atmosphere. However the ships really should have a lightspeed rating as well, since both are listed as being able to go to a jumpgate and mach 8 or 10 wont cut it in that respect.
Just to give a frame of reference on this, a spacecraft travelling at only 5% lightspeed is travelling at the equivalent of an aircraft flying at Mach 45! And such a craft would still take a minimum of 23 days to reach a jumpgate. Something travelling at a mere Mach 10 probably wouldnt have enough life support to reach a jumpgate.
Added to that, the term "mach" is an aeronautical term it really has no place outside of an atmosphere, since it is meaningless there. So based on the relative "days to jumpgate" ratings of the Runt and Republic craft, I propose the following speed and acceleration values:
Runt Shuttle Speed of 7% lightspeed (17 days to jumpgate), Acceleration of 56.7 hours / % lightspeed.
Republic Dropship Speed of 8% lightspeed (14 days to jumpgate), Acceleration of 43.4 hours / % lightspeed.
This keeps the time frame essentially the same, while still making them slower than the typical freighter.
On a related note, other craft which are atmospheric or lander grade should also be given atmospheric speed ratings, to determine how fast they can operate inside an atmosphere. Mach 8 10 is really pretty fast, even for a really high-tech spacecraft. Mach 4-5 is much more likely, especially for Tech 5 spacecraft like the Runt.
The Republic Dropship is unlikely to be rated at Mach 10 as well, since it has numerous turrets, is heavily armored, and is described as having an "awkward, bulky frame." Mach 2 or 3 seems more like it and that assumes that somehow Tech 7 craft can overcome some of the limitations of aerodynamics which prevent current aircraft from reaching those speeds unless they are very streamlined.