These chips of course still offered equivalent functionality in order to remain compatible. In later times, some of the integrated functionality was changed somewhat. Eg, AT and later PCs didn't use DMA channel 0 and timer channel 1 for memory refresh. On the original AT, there are still discrete 82xx chips, they just aren't connected. In integrated chipsets, these channels might actually physically not exist anymore.
I interpret this text from MSDN to indicate that channel 2 may also have been physically removed from some chipsets, because it was mainly used for the beeper. I never bothered to test PC speaker code on my modern systems. I know at least some of them still have a piezo on the board and boot up with a BIOS beep. I can only assume this is still the legacy PC speaker circuitry and PIT at work.
I don't think they would remove the 8253/8254 altogether, because channel 0 is used for timer interrupts, and a lot of software uses that (multitasking OSes used to use it for the scheduler for example).
I suppose there would be a modern replacement for that in ACPI, but I'm not really sure. Perhaps even current OSes still use it. I suppose checking the linux sources could answer that at least partially.
According to this page on APIC: https://en.wikipedia.org/wiki/Advanc...upt_Controller
The aperiodic interrupts offered by the APIC timer are used by the Linux kernel from 2.6.18 onwards to implement its tickless kernel feature; the legacy 8253 Programmable Interval Timer is no longer used by tickless kernels.