Here in Ireland, the term chapel is most commonly used to describe a Roman Catholic church. In most cases that would actually be a parish church rather than a chapel (ie a small church serving an individual family or ecclesiastical or other institution, such as a prison or hospital). So in Ireland the term chapel often does not really mean a chapel. If you asked anyone here what a chapel was though, they would mostly say RC church, before thinking of nonconformist churches, as is the case in England & Wales. (Nonconformists in Ireland tend to have meeting houses and gospel halls, rather than chapels).
As far as completing the civil register was concerned, it was up to the priest to decide what term to use to describe the building where ceremony took place. The form is pre-printed with the words “Roman Catholic “_________” of “___________” The priest is then free to enter church, cathedral or whatever he judges correct.
As far as deleting the word “Roman” on the civil marriage certificate is concerned, I have never seen that done before. That looks to me to be one individual priest's personal foible. In Ireland, the words Roman Catholic have been printed on those forms since 1864. I don’t know whether the wording was ever agreed with the church but I am not aware of any widespread objection to it in the past 150 years and suspect 99% of priests and their superiors are content with it.