You are right, the bootstrap just adds the skill at d4 for free. If I understand right, you will want the template to give a d6 to the skill, but charge you for both the d4 and d6. Try this:
Pre-Traits
Priority 5100
Code:
perform #traitadjust[skFighting,+,1,"Fighting d6"]
perform #resspent[resSkill,+,1,"Pay For Skill"]
Timing: Before Calc trtFinal
That should work if I understand you right. And you will still want to have the fighting skill bootstrapped in the group, but don't bother with the settings for it.