A PIN type of passkey is not used in BTLE as far as I understand the specification. Legacy Bluetooth devices used a fixed PIN passkey that was hardcoded into the device or entered by the application. This method of pairing was replaced by SSP (Secure Simple Pairing) in the next round of Bluetooth. BTLE came later and uses only SSP. The passkeys in SSP (when man-in-the-middle protection is enabled) are generated randomly by the Bluetooth software usually at pretty low levels. One SSP option is 'just works' and the entire passkey generation is internal. Great for the user but it is possible for Man-In-The-Middle (MITM) attacks. So in the end, for your Bluetooth LE application you will never use the 4-digit PIN.
So pairing with BTLE devices on the Android can be done in exactly the same way as one pairs standard Bluetooth devices. If the BTLE device is using an SSP option beyond 'just works', you will get a popup menu asking for you to either
verify a number displayed on the device and/or provide a number
that you must verify on the device (yes-no and display-only combos)
require that you enter a number that it displayed on the device
and/or display a number that you must enter on the device (keyboard)
The built-in pairing feature works for both BTLE and BT devices in spite of the fact under the hood the mechanisms are very different. BTLE devices transmit advertisements that client devices scan for (BTLE 'discovery') whereas BT devices scan for transmissions from the client (BT discovery) when it is looking for devices.
Alternatively one can use the BluetoothAdapter.startLeScan(LeScanCallback callback) method to scan for BTLE-only devices. This method will give you a list of BTLE devices that one can then select and attempt to connect to. In this scenario, your application will need to take care of pairing when it is required. Usually pairing is not required on BTLE devices until one attempts to enable notifications or indications. Service discovery, reading the Device Information Service and other tidbits often do not require pairing and if memory serves me right one can never require pairing for service discovery.
So to make life easier for my application I link to the standard Android provided tool for the discovery/pairing of any device that requires pairing and for those BTLE devices that do not require pairing (and there are a number of such devices) I use the startLeScan() APIs and do a BluetoothDevice.connectGatt() to one of the 'discovered' devices. If I use this approach and the device actually requires pairing I will get a security error. In theory I should be able to use the pairing APIs provided by Android to then pair with the device. Unfortunately my inept programming skills have led to the fact that I have yet to succeed in implementing it correctly.