The Oper of manuscript A (and the Aper of later manuscripts) is likely to be the modern Aber. "P" and ""b" are pretty interchangable in Old Welsh (See Welsh forms). Aper appears in a land grant by Hywel ap Rhys (c.850-c.885) though this is in the later Liber Landavensis ("The Book of Llan DÔv": 1133-13th C?)*). The use of O for A seems more unusual, and the trend was for Brythonic or earlier "a" to become "o", not the reverse*, possibly suggesting an early intermediate date.
Aber can refer either to the mouth of a river at the coast, or, more unusually, a river's confluence with another. For an example of the latter, see Gerald of Wales* (1197 CE: Book 1, Chapter II, in the latin).
Linn would appear to be Llyn ("Lake": See Welsh forms). However, there is no extant precedent for the use of Llyn to describe a coastal inlet, at least on the early nautical charts of Lewis* (1748 CE) or William* (1801 CE) Morris. The nearest is on Lewis Morris' map of the coast of Pembrookshire at Newport (Note, not Newport on the Severn), which shows a tidal inlet with the farm name Llwyn Gwair. However, this has a perfectly acceptable translation of "Mown/Hay Grove". In defense of its use, however, note that Pwll ["Pool"] was used to describe coastal inlets (for more details see Wonder 11).