Being well-educated and literate, Andrew Eldritch knew what gothic had meant for the couple of hundred years before post-punk rock, and in that context his assertion that the Sisters were not gothic makes good sense (especially as he self-identified more as a poet than as a songwriter)
The easiest way to illustrate this is by comparing his lyrics for "Alice" with Wayne Hussey's for "Garden of Delight". "Garden of Delight" is full dark gothic imagery — Take my hand and lead me to the Garden of Delight blah blah revelation blah windswept blah breathless blah — whereas "Alice" is a straightforward portrayal of the kind of screwed up modern girl who lives life through that Pre-Raphaelite filter: Alice in her party dress, she thanks you kindly, so serene, she needs you like she needs her tranqs to tell her that the world is clean.