I'm sure lots of engineers have used Concept for this purpose.
I assume you are using Load History analysis.
Alt Envelope factors are not used in Load History analysis, only the standard load (and pattern is used). The program manual, section 67.1 About RAM Concept’s load history deflection calculations mentions this.
Self-weight in Ram Concept is always applied. You would have to go out of your way creating a custom combination to have a case where self-weight is not applied.
Ultimately, I think you are asking if the deflection results in load history are linearly related to the external load and the answer is no. Cracking may take place during one load step and once cracks occur they never go away. Creep is also something that varies based on duration. You'll find other useful tips about Load History deflection here: 