There's no simple way to explain it all. Digital-to-Analog conversion is complex. I'll give you a very short summary. If you don't understand the basics of digital audio, you'll need to learn how regular PCM audio encodes analog waveforms at the very least.
A DAC has to re-construct the analog waveform using a number of samples taken of the waveform by the original Analog-to-Digital Converter (ADC). The samples are, more or less to a degree inaccurate as, as it is limited by the bit and sample rates, eg: 16/44.1 for "CD Quality". The DAC has to interpolate samples in between those taken to (reasonably) accurately reconstruct the analog signal. This is called "oversampling" (or "upsampling" sometimes). If you don't do this (ie: use the Pro iDSD's Bit-Perfect, or "Non-OverSampling"/NOS mode) you get a form of distortion that results in a loss of clarity. That is, how you perceive the soundstage will be smaller, and instruments will be less focussed.
Over the last couple of decades, there have been all sorts of arguments about how best to create a digital filter. Those arguments have included a focus on the "ringing" that you see around an impulse response sent to a DAC, even though impulse responses don't exist in music (they contain frequencies outside the sample rate, but people got hung up on this for a long while). That's what the GTO and Apodising filters are. Now here is where it gets funky. Some people don't like the sound with the various filters (massive quagmire, don't ask) and so prefer Bit Perfect (NOS) DACs. The particular DACs in the iDSD are sometimes used by people to build DIY non-oversampling DACs and are particularly good if NOS DACs are your thing.
However, with more recent advancements in the amount of computing power that can be put inside a DAC, it is possible to create much more accurate filters than are included with regular DAC (or filter) chips. That leaves us with the most technically accurate filter, the Transient Aligned, that uses the greatest amount of interpolation to most precisely reproduce the original signal.
Alternatively, you can set the Pro iDSD to re-sample everything to DSD512 or DSD1024. DSD is a 1-bit, extremely high-frequency sampling method. It has its own technical imperfections, but can produce results that sound very spacious, but less precise, depending on the DAC.
So what should you set? Whatever you like. There's no right answer.