It appears that more companies are appearing online seeming to offer the intermediary service that is required for small businesses to apply for IOSS. My understanding is that if we have an IOSS number Shopify is set up to calculate the VAT at checkout.
Most are prohibitively expensive but I did find one yesterday called CrossborderIT. They seem to be offering €19.99/month subscription and €1 per transaction. PLEASE NOTE - I have not been able to find any information about customer experience etc and am definitely not vouching for them just letting you know there are services out there at more affordable prices which don’t require integration with Shopify.