Yes, the new APT package update server is part of JetPack 4.3. You will still need to re-flash your device to get onto JetPack 4.3 from a previous version of JetPack, but once you are on 4.3 you will be able to upgrade to future releases by way of “sudo apt upgrade” (see here for more info)
To upgrade to JetPack 4.3, the entire device needs re-flashed with SDK Manager. It isn’t possible just to upgrade CUDA version.
If you are having problems with SDK Manager, you could flash the OS with the L4T BSP tools. Then manually copy the other packages that SDK Manager downloads (e.g. CUDA toolkit, cuDNN, TensorRT, ect) to your board and install them there by hand. Or once you have installed the JetPack 4.3 OS with the L4T BSP tools, you may be able to use the APT server to install the other packages (haven’t personally tried that method before)