Older motorcycle plates can be laid out in three lines, but there's no sane reason why that would be any more difficult to ANPR than the single line of most car plates.
My guess is that whoever planned it, went with cameras looking at the front of vehicles, and it didn't occur to them that this wouldn't work with motorcycles. Alternatively, this orientation could be deliberate, since it allows some degree of imaging of the driver, which may be useful in cases where identifying the driver may be necessary (although I'd presume that's primarily the responsibility of the vehicles registered keeper).
Either way, it's not a problem for cyclists, although the implication is that they'd have to be physically stopped, and that the only people who could legally do this, are police officers, who don't have the authority to impose FPNs (although presumably you could have police officers working in conjunction with others).
It seems unlikely that cyclists are going to be caught by these fines, since most of the time it's likely that they wouldn't be in the lanes, and when they are, it's going to be difficult to identify them. Conceivably someone could chase down cyclists (even a Police cyclist!), but that seems like a relatively low probability event.
