Design 5 to include the XC4x modules in the future?

No, the XC4x modules will only be available in version 6 and later. 

One of the main reasons for leaving many of the modules like MD3 and XA2 behind in the 5.x branch is to try send an early message that these are mature products, not recommended for new design. 

I wrote some more about it in the comments section on the IQANdesign 6 release.

I understand the intent here but this seems to have some unintended consequences. 

Some examples:

-We have at least 200 machines running in the field with MDL modules connected to 3 XA2s.  When the MDLs fail we offer a kit with a MD4 plus an XA2 to replace the MDL.  Ideally we would use a MD4 and a XC41 module but can't without replacing the other 3 XA2s... The additional mounting hardware, adapter harnessing, etc  already adds significant cost to the MD4 update kits so adding additional adapter harnesses and modules is not palatable.

-We have some machines that run with 8 separate XA2 modules located strategically around the machine.  It would be nice to slowly phase out the XA2s and transition to the XC4X series but with no software platform available to support that we are heading to the scenario where eventually a customer is going to need to replace 7 functional XA2s after one fails.  It is very difficult to justify this kind of expense to a customer.

It seems to me a software platform that could support both modules, would really help smooth out the transition period as the XA2 module becomes unavailable.

I have run into the same problem, We use a non-IQAN J1939 I/O module that is running on machines with 2 XA2 modules. This IO module was originally spec'ed to do 4-20 mA and a few other inputs that IQAN based modules did not support at the time.

We would like to replace the Generic J1939 modules with a XC43 on new built machines and as replacement parts to support existing machines but this is not possible with this limitation as we would then also need to replace the 2 XA2 units in the system.

Unfortunately this means we will continue using a mix of IQAN and Non-IQAN J1939 based modules in our machines for the foreseeable future.

I also see what the intent is here but it seems like this is unnecessarily limiting existing customers from implementing the XC4x products. Possibly a warning message "Not recommended for new designs" would also be effective.

Note that the XA2 is not in phase out, and has still many years to go, good to use on current design/production machines, as well as long term availability for spare parts and field replacements. 
However see this as an early information message that we do not recommend using XA2 in new designs, For new designs we advice to use IQAN 6 with the modern and flexibel MD4, MC4 and XC2 , XC4 series hardware.

See also Forum posts  :  https://forum.iqan.se/knowledge-bases/2/articles/2230-modules-supported-in-iqandesign-versions

Yes, this is also what our rep told us, that the XA2 will be sold and supported for quite a few years to come. My problem is that with the limitation that XA2 is stuck in the 5.x.x. branch and XC4x is limited to 6.x.x. This makes it impossible to use both modules in one machine system.

It makes sense to avoid using the XA2 in new designs, but we are trying to add a XC43 to a current design/production product as well as an option to support older machines that currently use XA2s to bring the whole control system under the IQAN line rather then mix with generic J1939 modules.

This limitation may actually force use to replace the XA2 with generic J1939 modules for new designs as this is the only way to ensure backwards compatibility and support for existing customer machines.