Nuno's answer points to a post on running ASP.NET MVC and WebForms side-by-side. There's a plethora of information out there on doing so, so I will skip that part of the question as it's not really Tridion-specific.

The crux of your question is this:

We would need to have two different BIN folders for cd_storage_conf.xml file since it for website A it would query only from Broker and website B (May Query from Broker + FileSystem).

You're right to imagine that running two instances of cd_storage_conf side-by-side could get hairy (if it's even feasible). The good news is you shouldn't have to do that at all.

cd_storage_conf gives you the ability to change your storage based on:

• Publication
• Item type
• File extension

You could, for example, store .aspx files on the file system like so:

<ItemTypes defaultStorageId="defaultdb" cached="false">
  <Item typeMapping="Page" itemExtension=".aspx" cached="false" storageId="defaultFile"/>
</ItemTypes>

Where defaultFile is the ID of one of your storage elements. Or, you could get more granular and specify by Publication:

<ItemTypes defaultStorageId="defaultdb" cached="false">
  <Publication Id="10" defaultStorageId="defaultdb" cached="false">
    <Item typeMapping="Page" itemExtension=".aspx" cached="false" storageId="defaultFile"/>
  </Publication>
</ItemTypes>

This should give you the flexibility you need and will mitigate the need for multiple "bin" directories.

You'll probably run into some bumps in the road but I see no reason why this couldn't work.

Nuno's answer points to a post on running ASP.NET MVC and WebForms side-by-side. There's a plethora of information out there on doing so, so I will skip that part of the question as it's not really Tridion-specific.

The crux of your question is this:

We would need to have two different BIN folders for cd_storage_conf.xml file since it for website A it would query only from Broker and website B (May Query from Broker + FileSystem).

You're right to imagine that running two instances of cd_storage_conf side-by-side could get hairy (if it's even feasible). The good news is you shouldn't have to do that at all.

cd_storage_conf gives you the ability to change your storage based on:

• Publication
• Item type
• File extension

You could, for example, store .aspx files on the file system like so:

<ItemTypes defaultStorageId="defaultdb" cached="false">
  <Item typeMapping="Page" itemExtension=".aspx" cached="false" storageId="defaultFile"/>
</ItemTypes>

Where defaultFile is the ID of one of your Storage elements. Or, you could get more granular and specify by Publication:

<ItemTypes defaultStorageId="defaultdb" cached="false">
  <Publication Id="10" defaultStorageId="defaultdb" cached="false">
    <Item typeMapping="Page" itemExtension=".aspx" cached="false" storageId="defaultFile"/>
  </Publication>
</ItemTypes>

This should give you the flexibility you need and will mitigate the need for multiple "bin" directories.

You'll probably run into some bumps in the road at an application level; however, I see no reason why this couldn't work fine.