First thing to know is for how long the right of way has been exercised by the neighbour.
If it is not so long as to constitute a true "acquired" right he is being a little cheeky and premature in seeking to register the right of way.
That said if he has been using it over a period of say 12 years or longer he might be acting sensibly and reasonably to protect his acquired right.
If only used for agricultural access OP is right to be concerned that it might be converted to another use at a later date.
If neighbour applies to the PRAI for the right and gets it OP might not be able to impose any constraining limits on purpose of use.
I would expect OP to hear from the PRAI if the neighbour makes an application to register the right of way.
OP could make representations or objections at that stage.
What this needs is for the OP to lay hands on every existing document relating to title and have his solicitor go through it all to see if there is anything lurking in the past that might impinge on the present position. I would be looking, amongst other matters, for any documentary evidence of prior agreements formed by predecessors in title to the respective properties. You would be amazed at some of the things you find in deeds bundles including information about things you never knew of. Solicitor time for sure.
If, after research, OP is satisfied that the neighbour may have good entitlement to register the right of way anyhow it might be possible to negotiate an agreed right of way in which is included the caveats OP wants as well as matters like responsibility for maintenance and repair. Be sure to reduce any such arrangement to a formal agreement and have it registered with Registry of Deeds as evidence of it's existence.
If the neighbour's application looks potentially tenuous but possible try selling him the right of way

The main thing to be avoided here is potential litigation over the issue. It would be preferable to negotiate that to litigate.....