Associating iRules with virtual servers that are managed by iApps is something that we've heard from the field before and so we've begun to integrate support for this right into the templates. That's the best fix for this situation, but I don't think the f5.http template has support yet. I'll look into that.
For now, I recommend that you not assign the iRules by hand after disabling strictness. If you do go that route, make sure that you test what happens if you re-enable strictness and make a change through the template to your existing application service. The behavior you see will depend upon the template.
Like I pointed out yesterday, it's usually not too much work to make a copy of a template and make some slight adjustments to it (like assigning iRules) so that you don't have to disable strictness. If you try that out, feel free to let us know if you run into any trouble or have any questions and we'll help you along.