You might consider using our Send Generated Codes feature to have us transmit each buyer's order details to a script at your end, which would then return info from your end such your VAT/PO/Order number(s) and have us insert that where you wish in the buyer's thank-you email and/or thank-you/download page. Normally this is used to obtain a software license/registration/key code to issue to the buyer, but it can be used for any other kind of plaintext output as well -- see details here:
One hitch with that approach is that it's product-specific, so you'd need to set it up for each product that would send their own separate thank-you emails, as the key value returned from your script could not be included in your Common Thank-you Email messages or the Common Thank-you Page HTML section of your E-junkie thank-you pages.
Similar to that, but without obtaining any output in return from your script, and possible to set up in common for all your E-junkie sales (rather than being product-specific), would be using our Webhook integration to have all the order details transmitted to a custom script at your end, which could then use that information and add further info of your own to generate an invoice email to the buyer directly from your end:
Unfortunately we have no way to add an extra comment field at checkout, especially for PayPal's checkout site which we have no control over from our end. If you could consider accepting card payment only (no more PayPal), you'd at least be able to customize the text labels for the optional Company or Address Line 2 field(s) in our secure card-checkout screen -- e.g., to prompt buyers to enter whatever additional details you require there. This customization would be in your E-junkie Dashboard under Manage Cart & Shop > Cart Preferences
