Choosing a preamplifier - synergy vs. matching components

Going with one brand allows you to double up on its strengths. Of course, you are also doubling down on its weaknesses. I don't think there are hard and fast rules and I don't think synergy is dependent on staying within a brand family. Impossible to reasonably compare two (or more) alternatives without hearing them. If you buy without an audition, staying in a brand family should be a safer bet-but still a gamble.

Thanks for all the feedback.

I can see that there's a lot to get in terms of synergy and then it requires to choose your brand carefully. 

I really like Audio Note but the price has amazed me quite a few times and I believe I can get more value for money proceeding with amplifiers from Yamamoto (Shindo, Audio Tekne, Sakuma (when it was available) Abbas, Swissonor and brands alike). As I wrote in my previous post I fully understand the cost of driving an enterprise with an enormous product catalogue where each item comes in many variations (Balanced, Signature, RIAA, Phono, Line, etc.). Therefore please do not interpret this as criticism of Audio Note, because I do adore the sound of their products. 

I’d put the amp in your system first, let it burn in for a couple hundred hours, and then see what you think.  If the amp, say, adds just enough warmth then adding their pre may be too much of a good thing.  Wait to see how it sounds and then see what direction sonically you wanna go with the preamp.  I’d always side with a separate phono pre — it’s too important, and rarely will the phono pre in a preamp compare to a good separate unit.  FWIW, and best of luck. 

Should system synergy be the priority, or can better sound be achieved by carefully selecting and matching individual components?

There is no universal truth.  Sometimes there is a significant synergy between preamp and amp like Audio Research, but non-matching brand success can be achieved with other brands.

Is it preferable to choose an integrated preamp with a phono stage, or is it better to go with separate components?

Integrated components save money in casework and cabling. It’s less flexible for future upgrades as both the preamp and phono must be changed together.  The sonic quality of the built in phono is also important.

Separate components cost more in casework and cabling, but is expected to perform better as external phono stages typically perform better than internal phono offerings.

How does a SUT (Step-Up Transformer) factor into this?

It changes the sonic profile usually subjectively for the better.  The OPs Denon 103R and at least the stone Koetsu are known to sonically benefit from SUTs which must be used with “voltage” phono stages.  Obviously a SUT is an additional expense, and SUT using silver can be pricey

Alright.

I see that there are positive sides to both directions, but perhaps I'm too much of a beginner to start matching components without having an idea what results it will bring beforehand. 

I'm corresponding with a gentleman who recommended me to look at Abbas Audio and his philosophy and approach to high fidelity is that of Sakuma and Shindo-san (that probably also makes it appeal to Yamamoto Sound Craft). 

Sticking with Yamamoto Sound Craft CA-04 is the convenient and obvious solution, but I was trying to see if I could gain some advantages by investing in another product that could compliment the VT-52 amplifier with greater and even better sound.