As an update it's all got a little messy.

I tried to pay £25 off the balance using a 3V virtual visa card, but it didn't work, stating that the billing address was incorrect. I tweaked it twice more (e.g. add county, with no luck). The address was entered exactly as shown on the 3V account. I'm not sure if this is a ba.com issue, or 3V issue. The 3V account showed that 3 x £1 authorisations had been taken off the card.

I then called BA who advised that any further attempts on that card would fail if attempted the same day, due to a 3 attempt limit. Luckily I had a second (untouched) 3V card to hand. The agent took the details and I requested £24 be taken (in case of any issue with a separate £1 authorisation). This went through first time, and he then took £1 to reduce that 3V number to zero. This was also successful. I will have to wait for the other card's balance to rise back to £25 before calling again to pay £25 with that card.

However, it was also apparent that the deposit I had previously "paid" when making the booking, £304.50, had not actually been taken. I was advised to call the finance team today to get that resolved.

Previously in MMB I saw that £304.50 deposit had been paid, with no additional payments, but after this call I saw that the deposit paid was £24, and additional payments had been made totalling £1.

I have today spoken with BA Holidays, who internally spoke to the finance team. They confirmed that the deposit payment had not been taken, and have taken it again. The available balance of the credit card has reduced accordingly.

However, in MMB the "deposit paid" figure has not changed from £24. The total holiday cost has instead been reduced by £304.50. Therefore the total due figure is correct, but the deposit figure is wrong. Is this normal?

I strongly suspect the "bonus" avios for the holiday booking may not post correctly, but hopefully that could be resolved with a call.

Therefore in my experience it is easier to give BA a call if you wish to pay with 3V virtual visa cards.

As an aside, I didn't realise that section 75 protection wasn't available when booking through a travel agent (BA holidays presumably included). However ATOL protection and suitable travel insurance should be sufficient for me. Because the credit card surcharge is only paid once, the avios collection benefits will easily outweigh the £4.50.