I honestly think some people overestimate how Troublesome a 20th Century All-Ireland Republic would be in the North. A large part of any animosity would be in regards to how Catholic the Republic would be, but the conservative policies of De Valera are in no way guaranteed to still come about; Collins in particular, while a personally devout man, would be unlikely to press the matter or try to "catholicise" the North, being in favour of a separation between church and state.
The big thing a lot of people seem to think is inevitable is some sort of reverse-Troubles, but the factors leading up to that OTL conflict are actually rather unlikely to come about on the other foot; the IRA of OTL was rather moribund with the failure of the Border Campaign until the late '60s, as the civil rights movement largely failed to reform Stormont. The level of discrimination and political disempowerment Catholics faced in that time in OTL might also happen to the protestants, but I find it unlikely due to Dublin's insistence on "all Irish being treated equally" or something to that extent. The Catholics in the North also won't feel as much of a need to "secure their future"; They are a province with a simply rowdy minority, rather than an outpost on a hostile island, like the Unionists of OTL thought (and think) of themselves.
The problems with comparing the situations of the Ulster Republicans and Ulster Unionists is compounded by comparing the attitudes of Dublin and London. London's attitudes towards the North have changed over time, but never have they considered it an integral territory as much as Scotland or Wales; in 1975 in fact, Harold Wilson was considering unilaterally withdrawing from Northern Ireland, leaving behind and independent state under the Crown, much to the dismay and horror of Dublin, who did not want that level of instability on their doorstep. Dublin on the other hand, from the beginning, will be invested in Belfast as much as the rest of Ireland; instead of a 50 year experiment with rather distant home rule, the north will be governed directly from Dublin as with the rest of Ireland.
Dublin will therefore be both harsher on active separatist movements than London was, while more lenient on Protestants than Stormont was, and more concerned with economic development than either. This combination makes a sectarian conflict like the Troubles far less likely under Irish rule
As for the first years of rule though, things could go either way, and are largely dependent on the nature of independence, northern integration/independence, and who leads the Republic; A conservative-led republic that occupies the North by force will naturally be far harsher than a reconciliation-minded man like Collins gaining unification through diplomacy, like in Kaiserreich.
