Python makes it easy to transform a sequence with a generator as long as no look-ahead is needed. utf16.UTF16.__iter__ is a typical example. Whenever a surrogate is found, grab the matching one.

However, grapheme clustering does require look-ahead, which is a bit trickier. Assume s is a sanitized sequence of code points with unicode database entries. Ignoring line endings the following should work (I tested it with a toy definition of mark()):

def graphemes(s):
  sit = iter(s)
  try: graph = [next(sit)]
  except StopIteration: graph = []

  for cp in sit:
    if mark(cp):  
      graph.append(cp)
    else:
      yield combine(graph)
      graph = [cp]

  yield combine(graph)

I tested this with several input with
def mark(cp): return cp == '.'
def combine(l) return ''.join(l)

Python's object orientation makes formatting easy for the user. Assume someone does the hard work of writing (once ;-) a GCString class with a .__format__ method that interprets the format mini-language for graphemes, using a generalized version of your 'simply horrible' code. The might be done by adapting str.__format__ to use the grapheme iterator above. Then users should be able to write

>>> '{:6.6}'.format(GCString("a̠ˈne̞ɣ̞ð̞o̞t̪a̠"))
"a̠ˈne̞ɣ̞ð̞"
(Note: Thunderbird properly displays characters with the marks beneath even though FireFox does not do so above or in its display of your message.)