Enjoy reading !! What else would you rather do on a Sunday ?
From what I gather, some round up on the individual product( line by line ) so they get the rounding up correct, where there are multiple products on the invoice and others will do it on the total, if the invoice is just for one product. If you round up on unit price at the start and you only have once product on the invoice, you are then charging the customer much more.
I have not studied the HMRC document, but from what I gather, both can be acceptable. The different accounting software used by companies, will produce different results.
Personally, I would go back to supplier 2 and ask why they are over charging VAT on an invoice for one product. Get them to look into this with HMRC and come back to you.