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As an educated guess, the H90 Program is still loading via the PC when the CC message arrives, a scant few milliseconds later (if that). Another speculation: the H9 – even with an older processor – is loading less than half of data that an H90 Program contains.
I suppose it’s possible to hold incoming MIDI messages in a buffer, delaying it long enough to slide into the MIDI stream shortly after the last command has completed. As a serial protocol, you’re bound to run into some limitations with MIDI vs. the power of modern processing.
I haven’t checked back your use case with either an H9 or H90. If I need a Program (or one of its Presets) to load bypassed, I re-save it with Bypass engaged. Then use an Act/Byp command as needed.