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Wasn't sure where to put this and couldn't connect with you on chat so here goes: this is the behavior I'm seeing (mentioned in the comments), note the problematic raggedness:

and this is my code for the counter cell dingbat:

SetOptions[EvaluationNotebook[], NotebookEventActions -> {{"MenuCommand", "Save"} :> (Scan[ Module[{nr}, SelectionMove[#, All, CellGroup, AutoScroll -> False]; nr = Length@ Select[SelectedCells[], Experimental`CellStyleNames[#] === "ItemNumbered" & (*1*)]; SetOptions[#, CellDingbat -> Cell[BoxData[ StyleBox[ToString[nr] <> " ", RGBColor[0.5, 0.5, 0.67, 0.81], FontFamily -> "Continuum Light", 15]], Background -> White]];] &, Cells[CellStyle -> "Subsection"] (*2*)]), PassEventsDown -> True}] 

As Kuba's comment fixes the raggedness:

SetOptions[EvaluationNotebook[],   NotebookEventActions -> {{"MenuCommand",   "Save"} :> (Scan[   Module[{nr},   SelectionMove[#, All, CellGroup, AutoScroll -> False];     nr = Length@   Select[SelectedCells[],   Experimental`CellStyleNames[#] ===   "ItemNumbered" & (*1*)];     SetOptions[#,   CellDingbat ->   Cell[BoxData[   PaneBox[  StyleBox[ToString[nr] <> " ",   RGBColor[0.5, 0.5, 0.67, 0.81],   FontFamily -> "Continuum Light", 15], Alignment -> Right, ImageSize -> 40]],    Background -> White]];] &,   Cells[CellStyle -> "Subsection"] (*2*)]),   PassEventsDown -> True}] 

I think when it's done each time you save the notebook it should be nice enough :)

SetOptions[ EvaluationNotebook[], NotebookEventActions -> { {"MenuCommand", "Save"} :> (Scan[ Module[{nr}, SelectionMove[#, All, CellGroup, AutoScroll -> False]; nr = Length @ Select[ SelectedCells[], Experimental`CellStyleNames[#] === "Input" & (*1*) ]; SetOptions[#, CellDingbat -> "(" <> ToString[nr] <> ")"]; ] & , Cells[CellStyle -> "Section"] (*2*) ]), PassEventsDown -> True } ] 

Ad 1. Cell style to count

Ad 2. Cell style whose parent group end "resets the counter"

You can use it in stylesheets too.

I think when it's done each time you save the notebook it should be nice enough :)

SetOptions[ EvaluationNotebook[], NotebookEventActions -> { {"MenuCommand", "Save"} :> (Scan[ Module[{nr}, SelectionMove[#, All, CellGroup, AutoScroll -> False]; nr = Length @ Select[ SelectedCells[], Experimental`CellStyleNames[#] === "Input" & (*1*) ]; SetOptions[#, CellDingbat -> "(" <> ToString[nr] <> ")"]; ] & , Cells[CellStyle -> "Section"] (*2*) ]), PassEventsDown -> True } ] 

Ad 1. Cell style to count

Ad 2. Cell style whose parent group end "resets the counter"

You can use it in stylesheets too.

Update from Question's Author:

Wasn't sure where to put this and couldn't connect with you on chat so here goes: this is the behavior I'm seeing (mentioned in the comments), note the problematic raggedness:

and this is my code for the counter cell dingbat:

SetOptions[EvaluationNotebook[], NotebookEventActions -> {{"MenuCommand", "Save"} :> (Scan[ Module[{nr}, SelectionMove[#, All, CellGroup, AutoScroll -> False]; nr = Length@ Select[SelectedCells[], Experimental`CellStyleNames[#] === "ItemNumbered" & (*1*)]; SetOptions[#, CellDingbat -> Cell[BoxData[ StyleBox[ToString[nr] <> " ", RGBColor[0.5, 0.5, 0.67, 0.81], FontFamily -> "Continuum Light", 15]], Background -> White]];] &, Cells[CellStyle -> "Subsection"] (*2*)]), PassEventsDown -> True}] 

I think when it's done each time you save the notebook it should be nice enough :)

SetOptions[ EvaluationNotebook[], NotebookEventActions -> { {"MenuCommand", "Save"} :> (Scan[ Module[{nr}, SelectionMove[#, All, CellGroup, AutoScroll -> False]; nr = Length @ Select[ SelectedCells[], Experimental`CellStyleNames[#] === "Input" & (*1*) ]; SetOptions[#, CellDingbat -> "(" <> ToString[nr] <> ")"]; ] & , Cells[CellStyle -> "Section"] (*2*) ]), PassEventsDown -> True } ] 

Ad 1. Cell style to count

Ad 2. Cell style whose parent groups are summarized

You can use it in stylesheets too.

I think when it's done each time you save the notebook it should be nice enough :)

SetOptions[ EvaluationNotebook[], NotebookEventActions -> { {"MenuCommand", "Save"} :> (Scan[ Module[{nr}, SelectionMove[#, All, CellGroup, AutoScroll -> False]; nr = Length @ Select[ SelectedCells[], Experimental`CellStyleNames[#] === "Input" & (*1*) ]; SetOptions[#, CellDingbat -> "(" <> ToString[nr] <> ")"]; ] & , Cells[CellStyle -> "Section"] (*2*) ]), PassEventsDown -> True } ] 

Ad 1. Cell style to count

Ad 2. Cell style whose parent group end "resets the counter"

You can use it in stylesheets too.