Will having a SDK/J Custom Auth app (ExternalLoginModule based) installed while an Android Cust Auth app installed case any issues?

Yes. When the custom authentication settings of both SDK/J and SmartSDK are enabled you will encounter issues. The Smart Operation Panel only supports one type of configuration; whether its exclusive for SDK/J or for SmartSDK, but not both.

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Custom Authentication Settings for SDK/J
SP5113-002 External Optional Counter Type
<Default> 0:None *
<Value> 1:Expansion Device 1

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Custom Authentication Settings for SmartSDK

SP5401-101 User Certification
<Default> 0*
<Value> 4

SP5401-111 User-Adoministrator Certification
<Default> 0*
<Value> 1

SP5401-230 SDK Certification Device
<Default >
<Value> 1