Hi, Nozomi,
I have a good news for you.
I found a way to achieve that manually.
Step 1.
download any mod from PSO2 MOD DB that seems to have opacity in texture
e.g.
Babydoll Lingerie over Baretop Dress
Step 2.
de-ice and extract the ".org.aqp" file through aqp2obj
Step 3.
For the mod you want to apply opacity (alpha),
rename this file ".org.aqp" and use it as the packer while repacking instead of the original .org.aqp file.
Step 4.
Done.
Notes
1. Textures with alpha work or not seems to depend on the org.aqp file largely.
2. org.aqp files also affect forms of models, may cause deforming and bone errors. (especially for those with long skirts)
3. This is NOT a perfect answer but chances are that it works in some cases.
Thank you for helping every time,
hopefully one day I will find a smarter way to do it.