What code sequences should we input, and what support should fonts supply? I think spacing and non-spacing marks may need to be addressed separately. For example, manual line-breaking may separate a visually following mark from its base letter, so what has the responsibility of not inserting white space for the typesetter's <NBSP, ZWJ, mark>? (One may be trying to reproduce the line-breaking and phrase boundaries of a manuscript written scriptio continua.) There may be similar problems with preceding marks if the trailing edges of the lines are to be set flush.
Line breaking can also apply to the holes used to string a document together. e.g. the holes punched in palm-leaf documents.
There is no standard way to suppress the display of the dotted circle in that situation, because it is being applied at the script shaping level by the shaping engine. Some common—non script specific—marks may display without the dotted circle because Unicode records spacing duplicates that have canonical equivalences to the mark character following a space character, e.g. ́ (U+0020 + U+0301). But shaping engine cluster validation is not defined by Unicode (and nor is it entirely consistent across shaping engine implementations).
Manual linebreaking can easily subvert normal orthographic rules. In the case of Indic scripts, linebreaking should never happen within an orthographic unit (cluster), and if a user inserts a linebreak within a cluster, in effect two clusters are created: one at the end of a line and one at the beginning of the next, each subject to independent cluster validation. In some cases, formatting control characters like ZWJ or ZWNJ can be used to affect the display of some components of the clusters, but this generally applies only to the consonant letters, e.g. one could use ZWJ to force display of a half-form at the end of one line, or of a phalaa (subscript or postscript) form at the beginning of the next like, but isolated marks are almost certain to trigger invalid cluster handling.
I don’t understand your comment about punched holes: physical artefacts of the binding of a document are not part of the text, so in what sense can linebreaking be applied to them?