I am surprised but I cannot seem to find much on this on the internet.
I did see something about needing to do it through a Web Role but I don't think that Azure does Web Roles anymore, I do not see the ability to add a Web Role in Azure Management Studio.
For clarity, this an Azure Website, not a VM. I need to Enable 32 Bit Applications in the Azure Website but I do not think I can after reading this: What is the difference between an Azure Web Site and an Azure Web Role
Do I have to create an Azure VM to Enable 32 bit applications in IIS?
If you need to install/register 32bit application, you have to use Web Role.
If you just want to run your website in 32bit mode, you can use Web Site. It must be in Basic or Standard mode. Then you can switch between 32bit and 64bit in management portal 'configure' tab.