Scoobster, I have done my IR(R) at Stapleford (can PM you details of my instructor) and started my CB-IR there, but had to pause for family reasons. Completed two years later at Aero Poznań in Poland and currently sporting "IR-SP-SE" in my licence.
In my particular case I only needed 10 ATO hours at the Aero Poznań: all 15 hours of my IR(R) training, 3 hours of Stapleford-ATO CB-IR, and 12 hours of my solo IFR flying under IR(R) qualification, were credited towards the 40-hour CB-IR minimum requirement.
I, too, have come across some instructors/examiners claiming that airlines look less favourably on those who achieved their IR via the CB Modular route, which I think is b.s. and an attempt to protect the business/extract more $$$. Most airlines will look for a first-time IR(A) skills test pass, and the test standards for that are exactly the same, whichever course you choose to complete.