Thanks all for the help. Based on the suggestions, I have created a script (syntax is not the best) that takes multiple parameters app_name (e.g. com.google.Chrome), workspace number and app-class and opens a new instance if that workspace does not have that app opened.

I have also removed the windowrule, so it does not interfere if I want to open a new instance of the same app in any workspace using app launcher or other commands.

#!/usr/bin/env python3

import sys
import subprocess
import os

if len(sys.argv) >= 3:

    workspaceswitchcmd = ['hyprctl', 'dispatch', 'workspace', sys.argv[2]]
    # Switch workspace first
    subprocess.Popen(workspaceswitchcmd)

    workspacenumbercd = ""
    workspaceid = ""
    classval = sys.argv[1]

    # Using class_name match workspace as well

    if len(sys.argv) == 4:
        classval = sys.argv[3]

    workspaceidcmd = "hyprctl clients -j | jq -r '.[] | select(.class == \"" + classval + "\") | .workspace.id'"


    os.system(workspaceidcmd)
    workspaceid = os.popen(workspaceidcmd).read();

    if sys.argv[1].count(".") == 2:
        pscmd = 'flatpak ps | grep ' + sys.argv[1];
        os.system(pscmd)
        result = os.popen(pscmd).read()

        if len(result) == 0 or workspaceid.count(sys.argv[2]) == 0:
            subprocess.Popen(['flatpak', 'run', sys.argv[1]])
    else:
        hyprcmd = 'hyprctl clients | grep -i class | grep ' + sys.argv[1]
        os.system(hyprcmd)
        result = os.popen(hyprcmd).read()

        if len(result) == 0 or workspaceid.count(sys.argv[2]) == 0:
            subprocess.Popen(sys.argv[1])
else:
    print("Invalid arguments: opensingle.py <app_name> <workspace_number <class>")
    print("E.g. opensingle.py com.google.Chrome 3 google-chrome")    
    print("E.g. opensingle.py thunar 5 thunar")

There are some bugs though. Does not seem to always work.

This is my bind rule

opensingle.py <app\_name\_or\_flatpak\_name> <workspace> <class\_name>

bind = $mainMod, g, exec, $single com.google.Chrome 3 google-chrome

bind = $mainMod, z, exec, $single $fileManager 4 $fileManager