Co-terminosity goes back to 1921, when the 10 Westminster constituencies (three of which were two-seaters) were used as the basis for electing the first 52 members of the Northern Ireland House of Commons, and again in 1925. Arguably it continued until 1948, as the boundaries for the Stormont single-seat constituencies all nestled within the previous Westminster constituencies, which were in turn linked to the local government districts (ie the counties, and Belfast City). In 1948 the link was broken, as the Westminster boundaries were revised and the two-seat constituencies broken up, without reference to where the Stormont boundaries were. However, all elections to regional bodies from 1973 on again took the Westminster boundaries as their basis; these days they elect six from each of the 18 constituencies, giving a total of 108 for no very good reason.
Three recent developments seem to me to spell the end for co-terminosity - not in the current round of boundary changes, but probably in the next or the one after that. First off, co-terminosity has been killed off in both Scotland and Wales. In Scotland, the number of Westminster seats was cut from 72 to 57 in 2005, but the 72 old seats still provide the basis for the 73 single-member seats in the Scottish Parliament (the Orkney and Shetland Isles elect two MSPs but only one MP) and will continue to do so after the next election when the number of Scottish MPs at Westminster will be further cut to 50. In Wales, the existing 40 parliamentary constituencies will also continue to be used for Welsh Assembly elections even after the number of Welsh MPs at Westmister is slashed from 40 to 30 at the next election. There is no reason for Northern Ireland to stick more religiously to keeping the boundaries aligned than the other devolved systems do.
Second, the new system of boundary revisions introduced by the present coalition puts the House of Commons into a state of perpetual revolution. The 650 MPs are to be cut to 600 at the next election. More significantly, the boundaries of the 597 non-island seats are to be revised every five years. Northern Ireland's small size and small number of seats mean that ripple effects of even quite a small population movement can be significant across the whole territory. In particular, it's quite possible that the number of Westminster seats allocated to Northern Ireland may change in future - had NI's electorate been only 0.5% lower when the calculation was made, there would have been only 15 seats to draw instead of 16 (and Scotland would have had 51 instead of 50). So Westminster boundaries are no longer going to be a stable frame of reference. It's maybe not a big deal to inconvenience one MP per seat, but if it's six MLA's as well then it will get tiresome.
Third, the long-postponed local government reform appears to be nearing legislative effect. This will create a new and hopefully long-lasting political framework for local councils, one which could equally well be used as the basis of Assembly constituencies. Using the published figures it is rather easy to allocate 108 Assembly seats among the 11 proposed new councils (Fermanagh and Omagh 7, Antrim and Newtownabbey 8, Lisburn and Castlereagh 8, Mid Ulster 8, Causeway Coast and Glens 9, Derry and Strabane 9, Mid and East Antrim 9, Newry, Mourne and Down 10, North Down and Ards 10, Armagh, Banbridge and Craigavon 12 and Belfast 18). One would probably want to split these into Assembly constituencies electing between 4 and 7 MLAs, and that would require an independent review process with public consultation; and population shifts would require some fairly regular revision. But, assuming that the new councils have anything resembling the 40-year lifespan of their predecessors, they will be a much more robust basis for electing Assembly members than the ever-changing Westminster seats.
I can't see this happening in the current round of revisions, which are too far down the road to stop. But in five or ten years' time, when the new local councils are fully established and up and running, and politicians (and activists) have started to get annoyed with the five-yearly revision of the Westminster seats, I suspect that the end of co-terminosity will be inevitable.