Currently when I'm playing a modded pack some modded blocks with transparency (like quark crystals) I can see the obfuscation after it. Because these blocks "obscure".

I don't think there's an easy way to catch all types of transparent blocks from every mod, but I think it's a good idea to add a config value to add block tags or individual blocks that shouldn't obscure, so that I can ensure there's not a mess of obfuscation behind these modded blocks.

This is already a feature.

hiddenBlocks a list of blocks to hide (Engine mode 1) or a list of blocks to use for obfuscation (Engine mode 2/3)
replacementBlocks is a list of blocks that will be obfuscated, but not used as fake blocks (Engine mode 2/3 only)

By default AntiXray will use the block tag #c:ores in hiddenBlocks. If you have special ore blocks that shouldn't be used for obfuscation you should manually add all blocks that should be used for obfuscation to hiddenBlocks and remove c#ores (or #forge:ores on forge). You can then add all blocks that should be hidden, but not used for obfuscation to the replacementBlocks list.