There would appear to be a correct way of refilling the system that requires various tools and equipment to do. This is taken from the workshop manual:
Filling with coolant: – Open valve -B- by setting lever in direction of flow. • The suction-jet pump reduces pressure in the cooling system to below atmospheric pressure. The display instrument needle must move to the green area. – Also briefly open valve -A- (turn lever in direction of flow to do this) so that hose on -VAS 6096- coolant reservoir fills with coolant. – Close valve -A- again. – Leave valve -B- open for a further 2 minutes. • The suction-jet pump will continue generating a vacuum in the cooling system. The pointer of the indicator must remain in the green zone. – Close valve -B-. • The needle on the gauge must stay in the green zone. The low pressure in the cooling system is then sufficient for subse‐ quent filling. Note ♦ If the needle does not reach the green zone, repeat the proc‐ ess. ♦ If vacuum drops, cooling system must be checked for leaks. ♦ The subsequent filling must be performed »slowly«. – Detach the compressed air hose. – Open valve -A- slowly. • Vacuum in cooling system causes coolant to be extracted from -VAS 6096- coolant reservoir and coolant system to be filled. • The coolant level must be above the max. marking after filling. – Remove cooling system charge unit - VAS 6096- from coolant expansion tank. – Fill coolant up to max. mark. – Install noise insulation ⇒ General body repairs, exterior; Rep. gr. 66 ; Noise insulation; Assembly overview - noise insula‐ tion . – On vehicles with auxiliary heater, switch on auxiliary heater for about 30 seconds. – Set temperature regulator to “HI”. – Switch off air conditioner compressor. To do this, press AC button. • LED in button should not light up. – Start engine and run it for max. 2 min. at a speed of approx. 1500 rpm. – Fill coolant up to the overflow hole of the coolant expansion tank while the engine is running. – Tighten cap of coolant expansion tank until it engages. – Then run engine at idling speed until radiator fan cuts in.
Ateca 2017 ➤ , León 2013 ➤ , León ST 2013 ➤ 4-cylinder petrol engine (2.0 l with direct injection, 4 V, turbocharger, timing chain, EA 888 III Generation BZ) - Edition 07.2018 1. Cooling system/coolant 211 Protected by copyright. Copying for private or commercial purposes, in part or in whole, is not permitted unless authorised by SEAT S.A. SEAT S.A does not guarantee or accept any liability with respect to the correctness of information in this document. Copyright by SEAT S.A. – Check coolant level. • When the engine is at operating temperature, the coolant level must be at the »weld seam« -arrow-. • When the engine is cold, the coolant level must be approx. 5 mm above the max. mark -arrow-.
Note This excessive amount of coolant level is necessary since the coolant level may decrease automatically due to bleeding process
I don't expect that to make much sense to you, but the last bit indicates it is done this way to avoid airlocks. By the looks of it they create a vacuum in the system be filling to prevent them from happening.