Sorry to hear there might be a known issue with multigigabit negotiation on certain switches, I'll check if I can find a status on it, but I'm sure it's being worked on. It's not "if Meraki decides to fix it" but what is the reasonable time to do an Engineering reproduction, root cause analysis, and write and deploy a firmware fix. Meraki has a good history of fixing similar bugs in record time compared to other vendors because of the power of cloud management... being able to see (on the back-end and on a world-wide scale) exactly how many products/customers are impacted, generate appropriate bug reports, pop Dashboard banners if applicable, and roll out firmware fixes in a methodical & controlled fashion.
To the 2.5Gbps point on the MR53, @PhilipDAth is correct and I'll add that Meraki did not arbitrarily choose the lower of two data rates and select 2.5Gbps versus 5Gbps. It's physics. The 3800 has a software-defined XOR radio and can do dual 5GHz, and a 5Gbps mGig rate is warranted/required. The MR53/53E/84 have one fixed 2.4GHz and one fixed 5GHz radio. So roughly speaking, running all 4 spatial streams (clients can't do this yet) at 80MHz channels with MCS9 (256QAM, 5/6 coding) and short 400ns guard interval, the theoretical max is 433.3 Mbps per SS, so roughly 1.7Gbps on the 5G radio. Add another theoretical max of 800Mbps on the 2.4GHz radio and there you've got a rather convenient AP max data rate of 2.5Gbps.
Even if we had 4x4 clients in the mainstream, the only way you'd really stress the AP to that level (today) is probably in a lab environment, and only with the most pristine RF conditions. Very unlikely in any typical deployment. Now you might be thinking what about 160MHz channels, fair point, as that takes us closer to 3.5Gbps theoretical for the 5GHz radio alone, and perhaps more of an argument for 5Gbps mGig on MR53/84. I'd argue that's also a rather large unknown. It will certainly be some time before enough spectrum is allocated to have a reasonable channel plan for the enterprise with 160MHz channels. And even longer before client devices with 4x4 and 160MHz channels go mainstream. By that time, we likely won't be designing with MR53/84 anymore and will be into next-gen 11ax APs.