Is a USB flash drive (AKA pen drive) basically equivalent to a USB SD card reader plus an SD card (or microSD card)? Or are they really two different beasts?
Related: Performance difference between SD and MicroSD cards?
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Is a USB flash drive basically equivalent to a USB card reader plus an SD card (or microSD card)?
They are "basically equivalent" only from the functional perspective of a data storage device that emulates an ATA drive.
Or are they really two different beasts?
Yes, they have very different capabilities.
A USB flash drive essentially emulates an ATA drive.
A SD card can operate in several modes other than just a block device to emulate an ATA drive. There are streaming modes to facilitate the high-speed recording of video.
USB flash drives have the expected USB standard 5Volt interface.
SD cards are low-voltage devices that use various interfaces with 3.3V and/or 1.8V.
Obviously USB flash drives use the USB protocol to transport the ATA protocol.
SD cards have their own interface protocol maintained by the SD Card Association, which is somewhat compatible with (but still distinct from) the MMC standard.
The SD card interface can transfer data in a one-, four-, or eight-bit mode at various rates. A SD card can also be accessed using a SPI interface instead of the SD card interface using the same pins of the card. (In fact, without information on how a USB-to-SD card reader actually works, you could assume that the SPI interface might be the simplest and cheapest conversion method.)
Accessing a SD card through a USB-to-SD card reader effectively conceals and/or disables all of these other capabilities/features. You would need an appropriate SD card controller to gain access to these other capabilities/features, but such a controller may only support a subset of the full SD card specification(s).
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