I have installed wacs v2.2.5.1541 (x64, ReleaseTrimmed) installed on the same server as MDaemon and generated the certificates without issue?
Enter email(s) for notifications about problems and abuse (comma-separated): peter@cfts.co
Plugin Manual generated source mail2.cfts.co with 4 identifiers
Plugin Single created 1 order
[autodiscover.cfts.co] Authorizing...
[autodiscover.cfts.co] Authorizing using http-01 validation (SelfHosting)
[autodiscover.cfts.co] Authorization result: valid
[mail1.cfts.co] Authorizing...
[mail1.cfts.co] Authorizing using http-01 validation (SelfHosting)
[mail1.cfts.co] Authorization result: valid
[mail2.cfts.co] Authorizing...
[mail2.cfts.co] Authorizing using http-01 validation (SelfHosting)
[mail2.cfts.co] Authorization result: valid
[webmail.cfts.co] Authorizing...
[webmail.cfts.co] Authorizing using http-01 validation (SelfHosting)
[webmail.cfts.co] Authorization result: valid
Downloading certificate [Manual] mail2.cfts.co
Store with CentralSsl...
Copying certificate to the CentralSsl store
Saving certificate to CentralSsl location D:\ssl\autodiscover.cfts.co.pfx
Saving certificate to CentralSsl location D:\ssl\mail1.cfts.co.pfx
Saving certificate to CentralSsl location D:\ssl\mail2.cfts.co.pfx
Saving certificate to CentralSsl location D:\ssl\webmail.cfts.co.pfx
Scheduled task looks healthy
Adding renewal for [Manual] mail2.cfts.co
Next renewal due after 2023/10/16
Certificate [Manual] mail2.cfts.co created
N: Create certificate (default settings)
M: Create certificate (full options)

I really like to get to the bottom of this? it clearly not a firewall issue, any advise would be good.
I have generated and tested the required ssl via wacs, all seems well, the issue seems to be somthing to do with mdaemon, but at least I have a usable fall back option now, was much easer than I thought it would be.
the steps to the working solution:
A simple Windows ACMEv2 client (WACS)
Software version 2.2.5.1541 (release, trimmed, standalone, 64-bit)
Connecting to https://acme-v02.api.letsencrypt.org/...
Connection OK!
Scheduled task looks healthy
Please report issues at https://github.com/win-acme/win-acme
N: Create certificate (default settings) <<
M: Create certificate (full options)
R: Run renewals (0 currently due)
A: Manage renewals (1 total)
O: More options...
Q: Quit
Please choose from the menu:
Running in mode: Interactive, Simple
Source plugin IIS not available: No supported version of IIS detected.
Please specify how the list of domain names that will be included in the
certificate should be determined. If you choose for one of the "all bindings"
options, the list will automatically be updated for future renewals to
reflect the bindings at that time.
1: Read bindings from IIS
2: Manual input <<
3: CSR created by another program
C: Abort
How shall we determine the domain(s) to include in the certificate?:
Description: A host name to get a certificate for. This may be a
comma-separated list.
Host: mail1.cfts.co,mail2.cfts.co,autodiscover.cfts.co,webmail.cfts.co
Source generated using plugin Manual: mail1.cfts.co and 3 alternatives
Installation plugin IIS not available: No supported version of IIS detected.
With the certificate saved to the store(s) of your choice, you may choose one
or more steps to update your applications, e.g. to configure the new
thumbprint, or to update bindings.
1: Create or update bindings in IIS
2: Start external script or program
3: No (additional) installation steps <<
Which installation step should run first?:
Plugin Manual generated source mail1.cfts.co with 4 identifiers
Plugin Single created 1 order
Downloading certificate [Manual] mail1.cfts.co
Store with CertificateStore...
Installing certificate in the certificate store
Adding certificate [Manual] mail1.cfts.co @ 2023/8/22 to store My
Scheduled task looks healthy
Adding renewal for [Manual] mail1.cfts.co
Next renewal due after 2023/10/16
Certificate [Manual] mail1.cfts.co created
N: Create certificate (default settings) <<
M: Create certificate (full options)
R: Run renewals (0 currently due)
A: Manage renewals (2 total)
O: More options...
Q: Quit
Please choose from the menu:
'<<' mark the options I used, once done just pop back into mdaemon and check it picked up the SSL's from the windows CertificateStore.

So now I can go back and get autodiscovery working :)