I think that example is more to do with track layout than a difference between tram and train. Although it makes a good point that infrastructure in city centres should be designed so that one small problem doesn't knock out the whole network.
With everything so densely packed though the only way I can think to reduce the knock on effects is space to terminate trams short in more areas, or more City Centre crossings.
Some things could include;
A proper re-design at Victoria with four proper, decent sized platforms if not six. (Provide two for terminating Tram-Train services to Rawthenstall, and Rochdale and Bolton via Radcliffe, or 'crowdbuster' >4 car services.
Any additional city crossings of infrastructure works should be designed to fit 6 carriage trams, a basic way of improving capacity. I know that nothing can be done about Market Street, Shudhill and it would be a challenge at Piccadilly Gardens, but them routes can be used by shorter 4 car diagrams, with 6 car diagrams using 2CC and 3CC.
If there is no chance of converting the Alty line BACK to heavy rail and providing terminating platforms in Manchester with integration of the CLC and a large interchange being provided at Cornbrook (This doesn't need to be Central Station, it can also be done by some new viaducting and using platforms that can be provided at Exchange / Victoria that would serve the CLC, Alty Lines and Chat Moss Lines via the grade seperated flow at Ordsall Lane High Level) With such a large interchange at Cornbrook, it can finally actually be classed as an interchange. (That would be one option, either converting Alty back to Heavy, and/or this
Metrolink 3CC:
Leave the current route from Deansgate at Deansgate Locks, new Viaduct over the junction to then run on new ramps down to street level on Whitworth Street West.
Station at Oxford Road, would possibly need to be on either side of the Oxford Road / Oxford Street Junction, but Whitworth St West isn't that busy on foot traffic so it should be OK to narrow up the paths and loose parking.
Continue down Whitworth Street up to the abandoned development at Princess Street, steal some of this development for 'Village' or 'Princess Street' station, two 6 car platforms, possibly also providing additional turn back sidings or a 3rd platform to terminate late running services here.
Continuing pretty much the same way, now either:
Continue on Whitworth St over the current junction complex at Chorlton St and Fairfeild St and into the current Piccadilly platforms.
or:
Continue down onto Fairfeild Street and cross over the 'taxi entrance' and basically steal the Short Stay Car Park for two or three terminating platforms linked into the existing metro link station by, well, opening the doors, traffic would be easy to keep clear as taxi entry is barriered so this can be used to keep the lines clear. At the actual traffic lights for the junction, these run on a rather simple scheme at the moment with a 1min20sec traffic and 30sec foot cycle, simply add in 30 secs for trams and provide a "Tram Only" lane for the length of Fairfeild Street, and re-do the pavements while you're there.
With 2CC and 3CC, if these are both compatiable with 6 car operation, only the quieter 4 car routes would run through the current 'core', the majority of these services starting or terminating at Piccadily.
5tph Bury - Piccadilly and 5tph Shaw - Piccadilly providing 10tph Vic to Pic
5tph Eccles - Piccadilly and 5tph Media City UK - Piccadilly?
There will be two routes quiet enough to make that happen, an additional 5tph will run from Deansgate to Victoria via the 1CC Core, from somewhere.
This would result in each CC route taking a much more manageable 15tph, with 6 car operation available for 30tph of these.
Since the main capacity constraint is going to be coming in from Cornbrook with 45tph not being unrealistic, this is why I'd be looking to provide as much capacity as possible in that direction. Either by bringing back Heavy Rail and providing the 2CC, then having 20tph per Core Route, that is handleable, and turn back and termination facilities at the new Cornbrook Metrolink station.
So if heavy did come back, it would take 10tph out of the tram routes, leaving the following available.
5tph Eccles
5tph Media City UK
5tph Trafford Park
5tph Manchester Airport
10tph East Didsbury
With 10tph still to spare, or a realistic level for the core to cope with 15tph per core route, with the numbers adding up nicely at Victoria too, 15tph from 2CC coming in and 5tph from Core 1 coming in with 20tph going out... (Plus the other 10tph from Piccadilly to send somewhere, but these could simply terminate at Victoria to provide nicer connections between the two)
Oh, and if anyone would care to alter the East Didsbury route by either building it with two track of space to the NE of the corridor (that they didn't, because they didn't think ahead!) or think later and move it over, the old route to Stockport could quite nicely be re-opened, providing a 2nd route from the Hope Valley and Hazel Grove avoiding Stockport Viaduct.
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