They truncated the route 'due to the amount of time taken to cross the city centre' but didn't then shorten the journey times as a result of no longer having to cross the city centre! The extra time in the new timetable, therefore the extra bus, is precisely that. More resource for a lesser service. If they are prepared to incur that additional cost, the previous route could have been kept, that additional resource inserted, everybody happy apart from those who benefit from the service terminating at Shudehill, whomever they may be.
Perhaps the time has been used to address congestion elsewhere on the route, there are some tweakings to the X41 intermediate timings. Perhaps the buses arrive early into Shudehill and in the opposite direction wait for time at intermediate points. I haven't used the new version often enough to form an opinion, certainly the X41 last week waited for time at Upper Broughton.
The cost depends on how Burnley and Pendle account for it. What's the going rate for a premium specification double-decker utilised only at peak hours? What's the cost of running buses empty between Burnley and Manchester? Are they accounting per bus required, per mile driven, per drivers hour?
Mileage is much the same. Previously 98 trips per day, currently 95 trips per day plus three empties, also a fourth journey truncated from Manchester - Burnley to a Rawtenstall - Burnley.
As it happens they appear to be short-changing their customers on a daily basis anyway, so are not incurring the cost of the additional vehicle. On a weekday daily basis one or both of the 1620 ex Shudehill / 1625 ex Chorlton Street departures does not operate. Often the 1440 ex Burnley, which forms the 1620 ex Shudehill does not operate either.