May one rely on the Shulchan Hatahor (Komarno) for halacha Lemaaseh?

Only when he is quoted by a recognized posek, and even that may just be brought to disagree, so always see it in the full context. The problem is that there are certain "maverick" ideas there which are definitely not mainstream in halacha and clearly not accepted, which you may not recognize as such, so don't learn it for practical halacha, for it may easily be confusing. On the other hand, when the Piskei Teshuvot or other authorities quote him l'ma'aseh, it is definitely legitimate.