Any PnP device that needs a com port (modems) will assign themselves the next available port, AFTER any other device.
If the motherboard has both ports active, then com 3 will be taken by the modem (usually) and a separate IRQ assigned. This is normal PnP stuff.
If you DISable the onboard ports (com 1 and 2 (A and B)) they are then "free" for devices to use.
USR modems do like to use com 5 (even though there isn't supposed to be such a thing), but that's the nature of PnP.
Com 3 isn't necessarily "cascaded" from com 1, but they CAN share an IRQ (causing modems to give the error "Port Already Open"

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Regardless of operating system, setting the BIOS "PnP Os Installed" to NO, can force peripherals to separate themselves better.
Things MUST be removed from device manager (in safe mode), before changing BIOS, fo that Windows can sort out it's resources better. Cheers,
Jim