If pluperfect is the past of the past, then this "if I will be late" is the future of the future. Here is a possible sequence of events:
1. A person says, "If I will be late, I'll call you". At this time, timing is still an unknown. This would be very strange in BE. We'd say if I'm late, I'll call you.
2. The person, not yet late, anticipates becoming late. At this time, the person "will be late", so the person plans to make the call. The person can say, "I will make the call because I will be late." This doesn't seem to be a case of 'If I will be late', at all.
3. The person makes the call, anticipating being late. What does he say?
4. The person is in transit later than planned. At this time, the person can say "I made the call because I would be late." Not a case of if I will be late, either
5. The person arrives barely on time due to an unanticipated lack of traffic problems. Now the person can say "Since I would be late, I called you. Soon I actually was late, but now I am back on schedule." In BE, I wouldn't understand this at all. If I've understood you correctly, we'd say something like: I called you because I thought I was going to be late. I was for a time behind schedule but now I've caught up.
If the person is already late in step 2, then "I will make the call because I am late" applies, and "If I am late, I'll call you" would be appropriate in step 1. But that is not quite the same situation.