@shefypattambi
It depends on how the project is/was being modeled the first place... The option to join them is there but that doesn't imply that projects should be modeled arbitrarily and then when it comes to structural modeling the engineer has to fix everything!!! if that is the case then you have an issue on your team
Revit offers tools and options which a user can use to how it best fits the situation but unfortunately 90% of Revit users believe that Revit has to think and model on their behalf...
The architect should know or at least be aware what the engineer needs and what makes his/her life easier and the opposite is also true...they will need to sit and discuss before either teams start placing walls and floors on the model (it's team work)...then later if some particular cases arise then they can be addressed individually; Revit also provides the tools to fix those; however, if the project is planned well, such cases should be minor. Not a whole project!!!
In terms of quantities...well; if you are going to apply the above on the whole project! then NO; the take-off quantities will not be reliable. My personal opinion; one better remodel the whole project properly instead of fixing it all...This is the exact same case similar to those who complain about floor finishes. Revit does not deduct quantities of floor finishes after one switch the join order of walls/floors. It is true that Revit offers an architectural floor which can host a structural core but who said it is right to model everything using Architectural Floor!!! Same applies to structural wall vs architectural walls
Development team (not just Autodesk's) might consider looking into improvements to certain functionality but not when it is "You need to fix Revit because I modeled this Project wrong and neither Revit realized and it let me do it nor did the tools fix what I did wrong"
When the time comes that Revit can think on the user's behalf 🙂 one wont need the user anymore!!! would be less headaches