I've come across this situation before.
Case 1
My client had an RCT audit. Inspector informed them because they did hold a payments card but had paid the money on a date prior to receiving it (a matter of weeks) technically the Revenue should treat the payment as being 65%. However, promises were made not to let it happen again and all was well. No charges or penalties
Case 2
I had a client who was a subbie who received payments from a main contractor prior to receipt of a payments card. The main contractor was audited and Revenue insisted that any payments made without cards be treated as being 65% due. They had to pay a lot of money to Revenue and issue RCTDC to the subbies, including my client. At that time, Revenue still paid out on RCTDCs and issued a refund to my client who repaid it to the main contractor.
Case 3
On a recent audit of a colleagues client, payments were made without a payments card on hand. Although Revenue admit there is no loss to them, they are insisting that any payments be treated as being 65%. They are also insisting on interest on penalties on late returns. ie. if a cheque issued in May but was only paid on June RCT 30 - interest and penalties are due. Having to treat payments as being 65% of the gross will probably put this man out of business. Resolution has not been reached.
In all of the above cases, subbies were all C2 registered and payments cards were applied for and on-hand but not until after the payments had been made. In some cases, only by days.
I don't think it is fair to say that this man had no regard for the RCT system. Sometimes people are just doing their best, or doing the nice subbie a favour by getting payment out to him. That is why you should listen to your accountant or book-keeper when we say NO to these requests.