Getting rid of your tight hip flexors is definitely something you need to work on. When the hip flexors are tight, the pelvis is tilted in an anterior direction. The lower back sways and the lower abdomen protrudes. The resulting posture gives the appearance of obesity even though you may be thin. The postural abnormality is known as lower cross syndrome and leads to back pain.
Tight hip flexors and hamstrings can lead to back pain when doing abdominal flexing exercises like sit-ups and hanging leg raises. When your doing sit-ups it is no longer recommended that someone hold the ankles. Holding the ankles only adds to the low back strain.
You are correct about the hip flexors action during the hanging leg raise. The hip flexors lift the legs and the abs act more as stabilizers for the spine. If your abs are weak and unable to stabilize, the back is going to be injured. Some trainers recommend lifting the legs to the chin to recruit the abs when doing captain's chair leg raises an exercise similar to the hanging raise.
The upper abs and lower abs are one muscle and many experts believe that you can not isolate the two when doing ab exercises. When doing flexing ab exercises, the hip flexors and abs work in tandem so isolating the abs would be difficult. Because of back problems, I minimize flexing ab exercises like sit-ups and crunches. I stick to the static core exercises like planks. I also have found that Pilates helps with ab development and prevents back issues.
You should work on stretching exercises for the hip flexor group to prevent postural abnormalities and back strain
An ACE commissioned study found the following to be the 10 most effective ab exercises. The article noted that doing reverse crunches will make you feel like your working the lower abs.http://exercise.about.com/od/abs/ss/abexercises.htm
Hip flexors get tight when chronically shortened as occurs in prolonged sitting. The classic example is someone that sits all day peering over his computer.
During leg raises, the flexors are going to lengthen when the legs are lowered to the floor. This should aid flexibility.