Thanks for debugging.
Sounds like it’s definitely the Product Option Plugins you mentioned.
Why are you needing to use Product Option plugins? Have you tried using our Product Add Ons plugin? That will let you manage add-ons to product similar to Attributes / Options but we know it’s compatible and stable. It’s also nice that it lets you apply add-ons to entire categories or tags of products, speeding up setup time a lot. I’m not sure if it will fit your needs but at least we know it does work.
One thing that the customizer does do is bundle product option data in a long encoded hash to send thru to be unpacked in the add to cart flow. If your Product Option plugins are modifying WooCommerce’s data format in some way it may be breaking the parsing or invalidating the JSON object in some way, I’m not sure, but that may be the issue with the third party plugin making changes to how WC normally sends thru product options and product add ons.
Do you have access to your server error log? If you can tail your server error log and then run the save / add-to-cart portion of the UX and catch what the error is, we may be able to put out an update that will fix it.