Yes, I meant to convey that the large differences in SAPT components between isomers are not immediately alarming, esp. if they reflect your qualitative expectations. At the SAPT0 level, I wouldn’t defend to the death the absolute value of any term (actually, benchmarking SAPT components even at SAPT2+3 suffers from lack of high-level reference calculations), but you can certainly pay attention to trends of the terms.
Perhaps this suppmat showing how SAPT components vary (even 10s of kcal/mol) in base pairs being shifted, twisted, rolled, etc. will be orienting? Relevant tables start at S26.