I'll comment only on USB ports. Others can advise on all the other features.
Both boards have equivalent USB 2 ports on the mobos, but do not include rear panel brackets. You can buy such brackets for 2 or 4 USB 2 Type A sockets at any parts store. Their cables plug into mobo USB 2 headers. Use these for slow-data-rate older devices.
The names have changed, but ALL USB 3 systems now are called USB 3.2 with a Genn suffix to label three current versions. Gen1 is the original of these at a max data rate of 5 Gb/s. NOTE that this is the max speed the communications subsystem can move data, and NOT the actual speed fo whatever device it is. For example, no mechanical HDD can actually access data on the disks at speeds over 5 Gb/s, so the communications subsystem can easily handle that rate. Gen2 has a comm subsystem max data transfer rate of 10 Gb/s. A few SSD's may exceed 5 Gb/s and thus use this faster rate. More fast devices may come soon. Gen2x2 has max 20 Gb/s rate, and there are no single devices that can do this yet, but they may come. The speeds and Gen labels are determined by the controller chips used for each, and of course by the abilities of the devices attached to the ports.
CONNECTOR details are important. The original common Type A connectors for USB 2 usually have BLACK plastic inserts in them supporting FOUR contacts. For USB 3.2 this Type A is modified to have those same contacts on a BLUE plastic insert PLUS FIVE more contacts at the back of a socket. Because of the similarities of design, you CAN connect either plug type to either socket type and it will work, but ONLY at the max speed of the SLOWEST component on that line, and at USB 3.2 Gen1 speeds ONLY if you have the USB 3.2 versions of Type A.
Among USB 3.2 Gen's, the Type A socket and plug system is quite OK for Gen1 speeds, and MAY or may not work at Gen2 speeds. For Gen2 performance, it is STRONGLY recommended that you use the new Type C sockets and plugs, and for Gen2x2 you MUST use Type C. If you use a Type A connection system on Gen2 or Gen2x2 it WILL work, but possibly only at the Gen1 speed.
So, with that for background, here's what those two boards have. The older ASUS MAXIMUS FORMULA XIII EXTREME board has two USB 2 mobo headers, each containing two USB 2 ports so you can connect those to rear or front USB 2 Type A sockets. It appears to have no such ports on its rear panel. The newer ASUS PRIME Z790M-Plus D4 board also has two USB 2 mobo headers providing two ports each. It does have two USB 2 ports on its own rear panel.
The ASUS MAXIMUS FORMULA XIII EXTREME board has USB 3.2 of all three types. Of these, eight on its rear panel are Gen2 Type A . Although the choice of Type A sockets for the Gen2 ports is not quite right, they may well work anyway. That panel also has two Type C sockets designated as Thunderbolt 4 ports. Such ports MAY be used for connection to USB 3.2 devices with similar performance, but I am NOT familiar with those details. Then it has two USB 3.2 Gen1 headers on the mobo, each providing two such ports. You can connect to these headers by cable a mounting bracket of some sort to expose those ports on the outside of your case, but the brackets for this are not included. Or, your case may have included such front panel sockets with cables to plug in here. The mobo also has two new Type E headers. One of these is for a single Gen2x2 port using a Type C socket, and you have to provide a front panel socket and connecting cable for this. Your case MAY have such a system. A SECOND Type E mobo header is fed by a different controller chip to provide two Gen2 ports; likewise you have to provide the connecting cable and pair of Type C front panel sockets. To get access to a Gen2x2 socket with this board you need to provide a cable and bracket for exterior mounting, UNLESS those rear Type C Thunderbolt 4 sockets can provide equivalent performance.
The ASUS PRIME Z790M-Plus D4 board has on its rear panel four USB 3.2 Gen1 sockets Type A, one Gen2 socket also Type A, and one Gen2x2 socket Type C. Again, the choice of a Type A socket for the Gen2 port may work anyway. In addition the mobo has two USB 3.2 Gen1 headers to connect to external sockets via cables and brackets (or to an existing case front panel socket). Of these, one is the current "standard" mobo USB 3.2 header with two actual ports in it. The other is a different new mobo socket type called Type E, and in more recent boards it is used to provide ONE Gen2x2 port. HOWEVER, on this board it is specified as performing only at the Gen1 speed and intended to connect to a type C external socket. It is likely that only one port is made available this way. Bottom line is that this board DOES provide one Gen2x2 socket and one Gen2 socket on its rear panel, four Gen1 Type A sockets on the rear panel, and up to three more Gen1 ports from mobo headers to be connected to exterior mounting brackets.
You will have to decide how many ports of what speeds you need. As I said, currently there are no HDD's able to use more than Gen1 speeds, and only a few devices that exceed that and need Gen2 speed for max performance. How soon faster devices to use the Gen2 and Gen2x2 speeds will appear is not clear yet. There is one type of configuration that can use that currently, though. IF you buy a USB 3.2 Gen2 HUB and connect to that two or more USB 3.2 devices (e.g., three external hard drives) those several devices will have to share the single USB 3.2 Gen2 or Gen2x2 data connection back to the mobo controller, and they will have enough data transfer rate to keep each of them at their max performance. I have seen Gen2 Hubs on the market now, but not yet any Gen2x2 Hubs.