I appreciate your fear, it’s valid, but yes, local laws in progressive locales will still prevail in a lot of cases, for the same reason why same-sex couples were able to get married in particular states before federal marriage equality went into effect. Most federal anti-trans legislation will simply allow states to do whatever they want, which leaves California operating pretty much business as usual. The ways in which Californians will be screwed is not the same as the way Ohioans will be screwed.
There are battles to fight here, surely, but California and New York will be better off than Alabama. Our legislative struggles here are far different than in more conservative areas. It’s not perfect, progressive cities aren’t all sunshine and free HRT, and we’re going to face many setbacks, but those setbacks will not impact all trans/queer Americans equally.