pgfmath: Integers without zeros, non-integers with zerofill (and fixed)

You can set key /pgfplots/table/@cell content from hook /pgfplots/table/assign cell content in order to define custom output markup for each cell. The argument of assign cell content is the unformatted data read from the input table. pgfmathifisint allows one to run conditional code that depends on whether said data represents an integer.

documentclass{article}
usepackage{pgfplotstable}
pgfplotsset{compat=1.17}

begin{document}
pgfplotstableset{col sep=comma}

pgfplotstabletypeset[
  every column/.style={
    assign cell content/.code={%
      pgfmathifisint{##1}
        {defmyOptions{}}%
        {defmyOptions{fixed, zerofill, precision=4}}%
      expandafterpgfmathprintnumbertoexpandafter[myOptions]
        {pgfretval}{myFormattedValue}%
      pgfplotstableset{@cell content/.expand once=myFormattedValue}%
    },
  }]{
0, 1,  -2,  1.23,  1.2345
}

end{document}

The hook /pgfplots/table/assign cell content is run inside a TeX group, therefore there is no need to manually clean up macros myOptions and myFormattedValue afterwards: this is automatic.

The following is equivalent and shorter, but has a bit more redundancy:

documentclass{article}
usepackage{pgfplotstable}
pgfplotsset{compat=1.17}

begin{document}
pgfplotstableset{col sep=comma}

pgfplotstabletypeset[
  every column/.style={
    assign cell content/.code={%
      pgfmathifisint{##1}
        {pgfmathprintnumberto{pgfretval}{myFormattedValue}}
        {pgfmathprintnumberto[fixed, zerofill, precision=4]
           {pgfretval}{myFormattedValue}}%
      pgfplotstableset{@cell content/.expand once=myFormattedValue}%
    },
  }]{
0, 1,  -2,  1.23,  1.2345
}

end{document}

Also possible, putting all the logic inside each @cell content (which might use a bit more memory, perhaps?):

documentclass{article}
usepackage{pgfplotstable}
pgfplotsset{compat=1.17}

begin{document}
pgfplotstableset{col sep=comma}

pgfplotstabletypeset[
  every column/.style={
    assign cell content/.style={
      @cell content={%
        pgfmathifisint{##1}
          {pgfmathprintnumber{pgfretval}}
          {pgfmathprintnumber[fixed, zerofill, precision=4]{pgfretval}}%
      },
    },
  }]{
0, 1,  -2,  1.23,  1.2345
}

end{document}