It is clearly stated on their specifications page:
Expansion Slots
4 x PCIe 3.0 x16 (single at x16, dual at x16/x16 mode, triple at x16/x8/x8 mode or quad x8/x8/x8/x8 mode)
1 x PCIe x4 (max at x4 mode)
What PCIe ports are connected to the CPU and which are connected via the PCH to a PCIe bridge is down to the manufacturer. Given the four slots I would expect 2 to connect to the CPU and two to the PCH. The motherboard manual may tell you which slots to use first to achieve a particular configuration.
Even an i7-9700 has only 16 PCIe lanes, so if you are going to be limited with your i3 (which might have other CPU performance related limits), then you will be limited with a better processor as well.
i3-9100 vs i7-9700 comparison
On top of that your PCH has a high speed bus to the CPU, and then splits out a further 24 PCIe lanes, 16 of which are apparently shared to the two x16 slots not services by the CPU.
Intel Z390 Specifications
It claims here that it only supports up to x4, but that may depend on specific parts and configuration. Asus might have a version or configuration that supports x16 and x8/x8, or might be using port multiplexers and buffers to "share" more ports, the Intel documentation will be for direct connection and Asus are likely using a non-standard setup.
This is the Layout you'll have:
Note the 16 lanes direct from the CPU (top left), and the 24 lanes from the PCH (middle left).
Found via Google Images and apparently from https://ark.intel.com/content/www/us/en/ark/products/133293/intel-z390-chipset.html (maybe one of the spec sheets)