Yeah it can be tough. What I would personally recommend is to use a tuner who has experience in tuning these cars. The problem is with a lot of tuners is that really to master a particular platform you really need to spend the time developing it, which most do not, they are just 'Flashers' who load a file onto the ecu without any understanding of the contents or if it is safe or not. Some other cars like Audis share the same ecu, so what you will tend to find is these tuners will use similar parameters from another engine and expect it to work just as well on another, while this can work sometimes, each engine is built differently with different compression ratios, components, etc.
Also the majority do not look/do not have the requirements or understand the actual parameters of the ecu, its rare you will find a proper tuner who actually looks at the tables and makes adjustments that way from the core of the code, which is the correct way to do it.
For me personally I limit the amount of cars I tune so I can perfect each one. Thats my motto anyway and its worked very well for me, Ive spent many hours developing and analyzing my tunes to make sure they deliver, but ultimately ensure safety.
Just to give people an idea, a tuned 12c/650 etc should make around 540-550 FTLB peak torque (Stock 460-470), you will only see rod damage around 650FTLB, as you can see there is a big difference there and plenty safe, also the other aspect of this is the liners, these are mainly damaged due to knock and excess cylinder pressure from a tuner using too much timing or an air fuel mixture that is too hot, so if these are dialed in properly, you wont have any issues and are within the manufactured limits of the engine so doesnt matter, For example Kevins 12c which runs in at around 900 to the wheels with Pure 900 turbos and tune.... Hes as happy as a larry.
@Ingenere no i dont really find them slow at all, but there are times when you get used to the power and the car begins to feel slow, but, lets put it this way, why leave all that power on the table when its safe to extract it? Everyone would like to have more power if its safe, its a no brainer. Including myself and I am very happy I did it, I am also REALLY not the type to have to spend mad money on an engine build either, so for me it was a big decision as well.