For build a Mini ITX with Ryzen 5 3400G, can I use Wraith STEALTH in place of Wraith SPIRE though it came with Wraith SPIRE but it not set in low profile setup.
Why do you want to replace the Wraith Spire with a Wraith Stealth?
Yes you can. They both are interchangeable but the Spire is more powerful than the Stealth.
Your Processor is going to run very hot with the Stealth (Weakest of all the AMD CPU Coolers).
Fixing cooling system problems
I reread your original post and you did mention why you wanted to install the weaker Stealth instead of the stronger Spire due to computer case size.
There are many 3rd party High TDP wattage CPU Coolers with low Profiles. One that comes to mind is Noctua. They have several models in which to choose. You just need to check to make sure it is strong enough for your processor.