Well both the cars have theri pros and cons,
both were the market leaders of theri era and even today you will find people who are crazy for these specific cars,
Margalla:
1300cc Sedan
more roomy, more power, may be a bit expensive to mantain aswell
Khyber:
1000cc Hatchback
not that much roomy but still one of the most roomy ones in the 1000cc category, 1000cc but having excellent power to weight ratio, wont let you feel underpowered, spares are a bit cheaper than margalla
and about the low ground clearance,
yes that is an issue with khyber but can be solved by placing spacers
but you keep in mind margalla is also not having that much ground clearance aswell
as you mentioned that trunk is not that much important so I would opt you to go for a Khyber but still the choice is yours,
have been driving the same car for a good 3~4 years now and my views are completely different