I don't know the answer, and would love reading some science on it, if anybody has a link.
If I had to guess, I'd guess that the legs were already malformed, and they caused the chick to be unable to zip properly. I highly doubt that 4-5 hours in any position can cause permanent damage, in the context of this chick spending 3 weeks in that egg, all squished and twisted up in there even in the normal position. If she was malpositioned, that must have started way before the zip stage, way back when she was first orienting herself within the egg. The extra few hours probably exhausted her and dried her out, making hatch even harder, but I doubt they did any actual damage. Especially if it's just 4-5. Some chicks get stuck much longer.
I'm interested in reading more on stuck chicks, assisted hatches and survivability though, if I can find actual research or other verified information besides anecdotal evidence. That's because my experience with hatch problems and assisting so far has been very depressing, in the long run. I've only assisted shipped eggs hatching in an incubator, because I figure there's too much human interference there that might be causing the problems, it's not a clear-cut matter of "nature" or "survival of the fittest". Shipping stress, incubator conditions etc. are all factors stacked against the chick that have nothing to do with its genetic fitness or future prospects. But so far all of my successful assists have produced chicks that went on to have problems, even if they hatched fine at the time. All of them had started zipping and zipped partway, like yours did, and got stuck. They all started drying out, even though my humidity was 80-90%, from all the other chicks hatching and increasing it. I'm guessing they dried out just from sitting open for so long. If they zip in the normal amount of time and your humidity is right, the membrane shouldn't dry out - it doesn't have enough time. But if the egg sits partly open for hours, even with high humidity you still have evaporation going on, and the membrane still dries out. Mine had dry, papery membranes that I had to dampen and peel off with tweezers, too. All of the chicks kicked their way out vigorously after I loosened the membranes, and looked like they had the strength and will to live. However, my excitement was short-lived in all 3 cases. One chick died at 4 days old from severe wry neck which developed and worsened very quickly after hatch; one died at 9 months old from heart problems (she was also developmentally stunted, even though she caught up to the others in size after the first few months), and one is still alive at 11 months old but very sickly, with chronic eye problems since hatch, chronic feather problems, and the only one to succumb to mycoplasma from a flock of 30+...