Adherence to ACAS recommended procedure is what an employment tribunal in UK uses as their benchmark. This includes several clearly defined steps, at each stage ensuring the employee knows what's happening and has the opportunity to 'course-correct'.
For example
1 employee commits some error or a repeat of an error
2 employer gives them their first informal warning and potentially puts them on a Performance Improvement plan (PIP).
3 Employee doesn't improve, meeting put in place and it is determined they haven't met the PIP requirements
4 employer puts things on a formal footing with a meeting to put the employee on notice of termination. even at this stage, employee has the opportunity to to appeal and show how they did meet PIP requirements
There could be a negotiation at this stage, eg leave by agreement, neutral reference etc.
what you have described is what many many employers try to do, which is to fast-track the Employee through the ACAS / aka stated company policy, skipping steps and preventing a fair process, just to get them out of the business.
First principles, don't resign, instead give ACAS the details of your 3 year and current problem with your annual leave and ask for their assessment as to whether they are reasonable in trying to terminate you. They shouldn't combine the past and present holiday issue into one reason to get rid of you.
go into the meeting with your head high. Be conciliatory, don't slag off their holiday booking system, say it was a genuine mistake and that you are very sorry for the inconvenience. If they try to terminate you, you can choose to accept that they want you out, but negotiate a good deal eg immediate termination in exchange for 3 months' pay as a settlement agreement (which will be tax free, so gives you time to find a new job so you have a cushion there) plus a neutral reference giving your years of employment and job post title, or you can object and say you want to find a way to retrieve the situation.
dont resign, by all accounts your misdemeanour is human error and really trivial, and you shouldn't be facing the sack. They're obviously trying to avoid redundancy, but they cannot be above the law on this. Plus you could go to tribunal for age discrimination if you can prove your age is a factor in their decision, eg, if there are younger employees who are given more leniency than you.