You use what you have. If you run 51 for 400, but your 100 is only 11.5, you run the 400. But I wouldn't say that height is no factor. Pavel Maslak is 5'9". Chris Brown is 5'10". So while there are international 400 athletes that are shorter than 6', they're still quite a bit taller than 5'5", and Maslak is quite a ways away from James and Merritt outdoors (being short is an advantage indoors).
There's a video on youtube with Dan Pfaff about speed endurance and race modeling, where Dr. Pfaff mentions that using short, choppy strides to accelerate "too fast" results in high energy use that costs you later in the race. He's talking about 100, but this may imply that shorter strides may compromise performance more in the 400, where energy management is much more important.
Now, there are really two things that control stride length. One is being taller, which you can't control. There other is strength and power, and you can control that to a point. I'd suggest that the OP spend time in the fall sprinting up steep hills, doing heavy squats, box jumps, and maybe short depth jumps (but the latter only if you have not had any injuries for at least 6 months), with the objective of increasing leg strength and stride length, and that may allow you to run 400 more efficiently. This is often a part of 400m offseason training anyway.