I am using "Publish Web Site" option to deploy DNN Web Site with Allow this precompiled site to be updatable ticked and other defaults which merges each folder output to its own assembly. 
On run-time I've got error:
 The base class includes the field 'ctlRoles', but its type (DotNetNuke.Modules.Admin.Security.SecurityRoles) is not compatible with the type of control (ASP.admin_security_securityroles_ascx) , that discussed in this thread.

I decided to use   Web Deployment Project with options Allow this precompiled site to be updatable unticked,
Output Assemblies/Merge each folder output to its own assembly   - ticked. to get thesimilar errors  during compilation, not during run-time.
It gave me a lot of compile error, mostly related to Providers\HtmlEditorProviders\Ftb3HtmlEditorProvider\ftb3 folder, e.g.

Error 1 'InitializeCulture' is not a member of 'ASP.providers_htmleditorproviders_ftb3htmleditorprovider_ftb3_ftb_createlink_aspx'. C:\FSDNN\Providers\HtmlEditorProviders\Ftb3HtmlEditorProvider\ftb3\ftb.createlink.aspx 1 1 FSDNN_deploy
Error 73 'AddWrappedFileDependencies' is not a member of 'ASP.providers_htmleditorproviders_ftb3htmleditorprovider_ftb3_ftb_insertsmiley_aspx'. C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\fsdnn\af85da85\fba2fc8\App_Web_9ejuthkb.2.vb 476 1 FSDNN_deploy.

I didn't analyze the errors, but it could be potential problems related to them.
I beleive that DNN development team should do the Web Deployment build and clean all related errors before each release.

 

After further investigation, the module was failing on a source version of 4.3.7.14114

Production was 4.4.1.26939
Staging that failed was 4.4.0.28454
Staging that worked was 4.4.1.26939

Recompiling by referencing the 4.3.7.14114 dll fixed my problem on the production box.  I do have "Specific Version" set to false in both module and SQLDataprovider projects.

Not that it matters at the moment, but I'm curious if I code a module in a dev-environment of the 4.4.1.26939 latest DNN version...is this issue going to reappear if the module is installed to earlier DNN 4.x versions?