Как активировать появление Checkbox в таблице QTableWidget

НИКОГДА НЕ ИЗМЕНЯЙТЕ код, сгенерированный Qt Designer, НИКОГДА.
Создайте другой класс, который наследуется от соответствующего виджета, и используйте созданный класс для его заполнения.

Я отметил для вам изменения, которые внес.

'''
from PyQt6 import QtCore, QtGui, QtWidgets
from PyQt6.QtCore import Qt
from PyQt6.QtWidgets import QTableWidgetItem, QTableWidget, QLineEdit
'''
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtCore import Qt
from PyQt5.QtWidgets import QTableWidgetItem, QTableWidget, QLineEdit


class Ui_MainWindow(object):
    def setupUi(self, MainWindow):
        MainWindow.setObjectName("MainWindow")
        MainWindow.resize(800, 400)
        self.centralwidget = QtWidgets.QWidget(MainWindow)
        self.centralwidget.setObjectName("centralwidget")
        self.tableWidget = QtWidgets.QTableWidget(self.centralwidget)
        self.tableWidget.setGeometry(QtCore.QRect(20, 70, 751, 192))
        self.tableWidget.setObjectName("tableWidget")
        self.tableWidget.setColumnCount(3)
        self.tableWidget.setRowCount(2)
        item = QtWidgets.QTableWidgetItem()
        self.tableWidget.setVerticalHeaderItem(0, item)
        item = QtWidgets.QTableWidgetItem()
        self.tableWidget.setVerticalHeaderItem(1, item)
        item = QtWidgets.QTableWidgetItem()
        self.tableWidget.setHorizontalHeaderItem(0, item)
        item = QtWidgets.QTableWidgetItem()
        self.tableWidget.setHorizontalHeaderItem(1, item)
        item = QtWidgets.QTableWidgetItem()
        self.tableWidget.setHorizontalHeaderItem(2, item)
        MainWindow.setCentralWidget(self.centralwidget)
        self.menubar = QtWidgets.QMenuBar(MainWindow)
        self.menubar.setGeometry(QtCore.QRect(0, 0, 800, 22))
        self.menubar.setObjectName("menubar")
        MainWindow.setMenuBar(self.menubar)
        self.statusbar = QtWidgets.QStatusBar(MainWindow)
        self.statusbar.setObjectName("statusbar")
        MainWindow.setStatusBar(self.statusbar)

        self.retranslateUi(MainWindow)
        QtCore.QMetaObject.connectSlotsByName(MainWindow)


    def retranslateUi(self, MainWindow):
        _translate = QtCore.QCoreApplication.translate
        MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow"))
        item = self.tableWidget.verticalHeaderItem(0)
        item.setText(_translate("MainWindow", "1"))
        item = self.tableWidget.verticalHeaderItem(1)
        item.setText(_translate("MainWindow", "2"))
        item = self.tableWidget.horizontalHeaderItem(0)
        item.setText(_translate("MainWindow", "Новый столбец"))
        item = self.tableWidget.horizontalHeaderItem(1)
        item.setText(_translate("MainWindow", "Метка"))
        item = self.tableWidget.horizontalHeaderItem(2)
        item.setText(_translate("MainWindow", "Расположение"))


class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
    def __init__(self):
        super().__init__()
        
        self.setupUi(self)

        
# ???        self.table = self.tableWidget
# ----------------------> v    ???
#        for row in range(9):
#            for col in range(9):
        for row in range(self.tableWidget.rowCount()):                         # +++
            for col in range(self.tableWidget.columnCount()):                  # +++
            
# ???                if col % 9 == 0:
                if col == 0:                                                   # +++
                    item = QTableWidgetItem('Item {0}-{1}'.format(row, col))
                    item.setFlags(
                        Qt.ItemFlag.ItemIsUserCheckable | 
                        Qt.ItemFlag.ItemIsEnabled
                    )
                    item.setCheckState(Qt.CheckState.Unchecked)
                    self.tableWidget.setItem(row, col, item)
# ???                    self.tableWidget.setItem(row, col, 
# ???                        QTableWidgetItem('Item {0}-{1} \'.format(row, col)))
                else:
                    self.tableWidget.setItem(row, col, 
                        QTableWidgetItem(f'Item {row}-{col}'))
     
        

if __name__ == "__main__":
    import sys
    app = QtWidgets.QApplication(sys.argv)
    '''    
    MainWindow = QtWidgets.QMainWindow()
    ui = Ui_MainWindow()
    ui.setupUi(MainWindow)
    MainWindow.show()
    '''
    w = MainWindow()
    w.show()
    sys.exit(app.exec())