Interesting question.
To give an answer, we need to go back to the 1970s...
The Rapid Transit system was always planned to penetrate Newcastle City Centre, while making the most of the existing railway alignments to North and South Tyneside and towards the airport (Bank Foot). Throughout the seventies, the city centre also underwent some major redevelopment, notably the construction of Eldon Square shopping centre and the Central Motorway East. As its name suggests, there was also a plan for a Central Motorway West, which would have been constructed on what is roughly today's St James's Boulevard. There was also to be an east-west central motorway link, running largely underground. This was planned to be underneath what was the "old" Eldon Square Bus Station (which would have been a three-level construction: a motorway in the "basement", the bus station above and the shopping centre above that). (This, incidentally, also explains why the alignment of the "old" Eldon Square bus station appeared strange, failing to connect with Percy Street at what would have been a more logical 90 degree angle, but being skewed). The east-west motorway link would have emerged east of the Central Motorway East and followed New Bridge Street. After crossing the Ouseburn, the motorway would have skirted through Byker, following the alignment of the Byker Wall housing development (which also explains why the Byker Wall has fewer windows on its north side, and balconies on the south).
Are you still with me? Good.
The original Metro plan had been to use exclusively two of the four tracks of the ECML through Heaton, just as the coast railway line had. This was deemed necessary because the original plan envisaged a Metro train every two and a half minutes, half of which would have terminated at Wallsend, while one train every ten minutes continued to North Shields and the remaining train ran right round the coast loop. However, BR indicated that this wouldn't leave them enough capacity for all their traffic on the remaining two tracks. BR was also foreseeing the eventual electrification of the ECML (there's a whole other story involving why Metro doesn't use 25Kv AC for its power, which I'll leave for another day).
Construction of the Central Motorway East had begun, and could have threatened the possibility of the Rapid Transit System ever being built. So the Passenger Transport Executive agreed to put up the money so that two box tunnels could be built beneath the motorway, at Jesmond and Manors, to accommodate Metro, should it ever be built. Which explains why the tunnels there are the shape they are, rather than being circular bores (I hope this isn't boring you!). As the Central Motorway East is diving down into an underpass beneath 55 degrees North (formerly Swan House) to reach the Tyne Bridge, putting the Metro box tunnel any further south would have caused Metro to be very deep here, bearing in mind that the plan was for Metro to reach the ECML alignment. And if you go to Manors railway station, you'll realise that the station is, essentially, built almost atop a viaduct here - Newcastle at one time had other deep denes, like Ouseburn, running down to the river - the one here was Pandon Dene.
So, that's how Manors Metro ended up being built where it was.
The issue of interchange between Metro and BR here was not overlooked. However, the number of trains calling here has diminished over the years, although it is still an important weekday commuting halt.
Regards
eezypeazy