>>9,10
There are various nuances that people (such as yourself as an example) do not understand about GPLv3. This confusion is based upon the idea that GPLv3 software causes all additions to the software to be permanently and exclusively relicensed as GPLv3; this confusion is a false interpretation of GPLv3.
1) Publisher A conveys program P under GPLv3
2) Publisher B conveys module Q under a licence that is compatible with GPLv3 but is not actually GPLv3.
3) Publisher C conveys program P combined with module Q: this is program R and program R is GPLv3 by implication of program P being GPLv3
Note that it's possible for publisher A, publisher B, and publisher C to be the same legal entity, it's possible for them to be different legal entities, however this distinction doesn't have any meaning as far as the GPLv3 is concerned.
You are correct in your assessment that module Q within program R is licensed under GPLv3. The subtle thing you need to understand is that this is true for the context that module Q forms a combined work with program P. One implication of the GPLv3 is that the licensee publisher D is allowed to delete program P and then publisher D is allowed to convey module Q under GPLv3, however it isn't mandatory to convey it as GPLv3 when doing so; note the context is that the module Q has been divorced from program P meaning it doesn't form a combined work under GPLv3 any longer. The license of module Q from publisher D remains according to the licence from publisher B.
So the "relicensing" or "viral" aspect of the GPLv3 only has meaning within the context of the "combined work with GPLv3 work". When you divorce it completely, the combined work mandate doesn't apply to the non-GPLv3 software.
Now this brings me to lib/html.scm, deps/httpio.scm (program P in my analogy) being AGPL while the rest of SchemeBBS (module Q in my analogy) is liberally licensed under MIT license and together they form the combined work SchemeBBS (program R in my analogy). While it's correct that the combined work SchemeBBS is AGPL, the module Q portions have never stopped being free software under MIT when isolated from program P. Licensees of program R are allowed to delete lib/html.scm (program P) then convey the module Q portions under the MIT license without the AGPL mandates. The meaning of the AGPL allows for this scenario.
This means the MIT licensed portions of SchemeBBS are not in conflict with the AGPL (and GPL) combined work of SchemeBBS.