I used Starling Virtual Card and funds were taken 3 days ago so I think all is fine.
At the VFS office, they placed the form in a separate envelope sealed with sellotape and I think we both signed across the seal, there might have been a stamp as well.
Just for reference:
5th March Appointment
5th March Received Email Confirmation Application sent to UK
12th March Payment taken.
15th March Acknowledgement via SMS from HM Passport that they have got my application.