Your initial method for addressing this problem is the most common for what I am use to. Simply put, assign your company's part number to everything. If it is not the same, it is a different number. The second part of your solution, common description rules, is the searchability solution.
If the part in an assembly is not a valid part number*, the assembly is not valid and should be flagged in Windchill to be corrected.
I am not in favor of intelligent part numbers because there simply is no end to it. Yes, it helps searchability but where do you draw the line for distinction. And what happens when your company merges with its partner with a completely different system.
One you develop a standard you want to work with, stick to it. Hire a contractor to clean up your database. Bring them in-house and tell them what they need to do... and what they will be responsible for. Be prepared to initial oversight to make sure your data is not getting seriously corrupted at next level assemblies. Everyone who had created the mess can help clean it up. But the in the end, there is a single focus where the work is getting completed.
And you might consider some standards in how models are created. Level of detail can be a real stickler for some and an annoyance to others. Do screws really need threads? Do you want family tables or simplified reps to manage these as optional? All OEM hardware and components have huge variance in CAD use. Personally, I like detail in my PCB connectors while other find 2 block to be sufficient. Make some rules and enforce them.
And then decide on how compliance is managed. How do you safeguard the "approved" files so they don't change out of the blue and blow up assemblies during an engineering change process.
In my many years, I've always found myself in the middle of these conversations. No outside company will give you exactly what -you- need. They tend to offer what they -have- no matter how good their pitch.
I don't know where you are located, but if your enterprise would like some insight as to the best way to proceed beyond what I posted here, please feel free to contact me through the private message. This really isn't too difficult. It just takes time and effort to get on the right path for your business profile.
* some file naming variability is likely required but it should follow an established convension.
