I think the reason we don't see many low-to-midrange MCU + FPGA combo devices is that as long as you don't require huge bandwidth of MCU <-> FPGA link, it's fairly trivial to just place any "normal" MCU with any "normal" FPGA - at this performance bracket MCUs typically don't require elaborate PDS setup, nor connection MCU <-> FPGA is any sort of problem (because it typically doesn't require high bandwidth, you can make do with any commodity bus like I2C, SPI, etc.), while having a wide choice of possible MCUs allow to optimize a design according to design priorities (performance, size, cost, toolchain/libraries quality, TTM, etc.). Compared to higher-end setups with full MPU and FPGA, here connection bandwidth might very well become a limiting factor, especially since for some unknown reason SoC manufacturers typically provide very limited choice as far as this connection is concerned - like a single line of PCIE 2 at only 5 Gbps in each direction, and these higher-end MPUs typically require quite complex PDS setup, which goes in addition to what FPGA itself requires.
Just to give an idea, according to Zynq TRM CPU <-> FPGA interconnect is facilitated by over 3000 connections. Obviously it's not feasible to implement that kind of interconnect with discrete devices.