Yes, it seems that SPM's convention for naming anatomical orientation is different from that of acpcdetect and NIFTI.  

What acpcdetect and NIFTI calls RAS means +x=R, +y=A, +z=S

What SPM calls LPI means-x=L, -y=P, -z=I

They are talking about the SAME anatomical orientation.

Your approach of relating the header matrices in your original images to the header matrices updated by acpcdetect seems reasonable, although I can't help you with the details.

Good luck.

Babak