Esolang-Comment-Template-Generator

Java 10, 189 159 bytes

s->c->{var r="";int p=0,i;for(var a:s.split("\\|")){for(i=p;i-->0;r+=" ");r+=a;for(p+=a.length();i++<s.replace("|","").length()-p;r+=" ");r+=c+"\n";}return r;}

-30 bytes converting Java 7 to Java 10 and optimizing the loops.

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Explanation:

s->c->{                     // Method with String & char parameters and String return-type
  var r="";                 //  Result-String, starting empty
  int p=0,                  //  Position-integer, starting at 0
      i;                    //  Index integer
  for(var a:s.split("\\|")){//  Loop over the parts split by "|"
    for(i=p;i-->0;r+=" ");  //   Add `p` amount of spaces to the result-String
    r+=a;                   //   Add the current part to the result-String
    for(p+=a.length();      //   Add the length of the current part to the position-integer
        i++<s.replace("|","").length()-p;r+=" ");
                            //   Add the row's trailing spaces to the result-String
    r+=c+"\n";}             //   Add the character and a new-line to the result-String
  return r;}                //  Return the result-String

Retina, 35 34 bytes

Byte count assumes ISO 8859-1 encoding.

\|
·$'¶$`±
T0-2`·±|p`___ `.+±.|·.+

The two input strings are separated by a space (which is unambiguous since we know that the comment delimiter is always a single character).

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Pyke, 31 28 24 bytes

\|cDslF2l-hd*Q+Zi:il?+ZK

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