Setting layer visibility in standalone QGIS Python script

Question

I've been writing a standalone Python script that calls QGIS 3 libraries to draw stuff in a QWidget. I'm trying to change the visibility of layers based on a callback, but it doesn't seem to work.

Here is an MRE of the problem:

#!/usr/bin/env python3
import argparse
import os.path
from qgis.core import (
    QgsApplication,
    QgsProject,
    QgsVectorLayer,
    QgsWkbTypes,
)
QgsApplication.setPrefixPath("/usr/bin", True)
from qgis.gui import (
    QgsMapCanvas,
)
def main():
    qgs = QgsApplication([],True)
    qgs.initQgis()
filepath = '/PATH_TO_S57_FILE/S57.000'
layer = getALayerWithGeometry(filepath)
print(layer.name())

canvas = QgsMapCanvas()
canvas.show()

QgsProject.instance().addMapLayer(layer)
canvas.setLayers([layer])
canvas.setExtent(layer.extent())

layer_tree = QgsProject.instance().layerTreeRoot().findLayer(layer)
breakpoint()
# vis_target = not layer_tree.isVisible()
# layer_tree.setItemVisibilityChecked(vis_target)


def getALayerWithGeometry(filepath):
    dataLayer = QgsVectorLayer(filepath,'S57 data','ogr')
subLayer_str = dataLayer.dataProvider().subLayers()
for (iSubLayer,subLayer_str) in enumerate(subLayer_str):
    subLayerDefs = subLayer_str.replace('!','').split('::')

    id_ = subLayerDefs[0]
    objectAcr = subLayerDefs[1]
    geometryType = subLayerDefs[3]

    composedURI = f'{filepath}|layerid={id_}|geometrytype={geometryType}'
    layer = QgsVectorLayer(composedURI,f'{objectAcr}({geometryType})','ogr')
    if layer.geometryType() not in (QgsWkbTypes.UnknownGeometry,QgsWkbTypes.NullGeometry):
        return layer


if name == "main":
    main()

Then at the breakpoint:

vis_target = not layer_tree.isVisible()
layer_tree.setItemVisibilityChecked(vis_target)

• This attempts to use setItemVisibilityChecked() after a QgsProject.instance().layerTreeRoot().findLayer() call described here and here.
• Setting layers with canvas.setLayers() works, but I would like to avoid that if possible.