Hey there. I read your question and I have been thinking about a response for you. It seems like you’re after feedback as well as answers for a complicated question that I also had when I began using hookpad years ago, so I’ll do my best. I have listened to your song - nice work. I can definitely identify the hookpad instruments as well as some of the rhythm settings on the instruments. There are a few things you can do to differentiate, if this is a concern for you.
First - Hookpad doing 90% of the work seems too much and possibly why you might not be getting the results you want, same as how you wouldn’t expect 90% of the process of drafting a house design to be possible in something like Floorplanner - at some point you have to involve an architect, a builder etc, so you can make sure it doesn’t fall down on your head. That architect/builder is you! Maybe 10% of the work is done in hookpad for me. It’s a fast way to get ideas out of your head and to fill in the gaps, so your concepts can develop, but not a complete solution.
Hookpad draws from much collective theory and convention, especially regarding chord progressions, as drawn from popular music. Many of the suggested progressions can be found in common songs - they are successful, and they sound good, so people use them. They don’t belong to anyone - the difference is how the progression exists in relation to other parts of the piece (is there a key change? dynamics? changes in rhythm?), and how it is recorded, played/performed, mixed, and if lyrics are added. So no, I don’t think chords or chord progressions are identifiable. You can pick up a “beginners songwriting” book and it will tell you much the same thing. Turn on a pop radio station and you’ll hear it too. They are popular because they can be really compelling. (I believe that’s what the “hook” in hookpad refers to.)
Also - you don’t have to necessarily loop your progressions, or restrict yourself to a four measure progression. You can vary the progression in each phrase as well. This adds interest.
The arpeggio that is introduced in the first section of your track, for example, is an established technique - when doing this on an instrument, you’re playing a chord, but one note at a time. But, to address the sound on the recording, it’s a low quality midi instrument playing it - there isn’t any realism. This can be an effect in itself (such as when people create music using old game console soundfonts - NES chiptune, or Wii sounds - for a particular effect), or it can sound like you used a low quality digital instrument. Seeing as not many people would have sweet nostalgic feelings for hookpad, it would probably be the latter.
Hookpad instruments can sound quite generic (I wouldn’t expect realistic instruments from a compositional tool - representative is enough) - would you consider using some different VSTs for a wider and more distinctive sonic palette? I see you use Spitfire. Their other virtual instrument VSTs (available for free) are really good - give them a try.
If you’d like to explore some interesting sounding synths (for free), I can recommend Feldspar, delamancha, and Surge.
I would also like to say - making bizarre fx chains that sometimes crash your daw can make some truly heavenly sounds, and can really transform virtual instruments. So don’t be afraid to get a bit creative. (I actually cannot open the project file of my most-listened song of all time, outside the DAW’s safe mode, for this reason.)
Another point on the arpeggio and other features - if it sounds a bit “canned”, it’s because it is being sounded as-is, highly literally, and unedited. I think people can tell when something sounds “sequenced”, or overly quantised and homogenous, and can be put off by that.
Would you consider using your DAW’s “humanise” setting, if there is one? Perhaps lengthening and shortening individual notes (even within chords) to your preference? Deleting or adding notes? Moving them around?
Simulating a performer’s mistakes can be really powerful when making “computer music”. I know I make a lot of mistakes playing my instrument that people think are intentional and impressive flourishes. I am working on my urge to correct them 
Hearing about mixcraft really takes me back, by the way! I didn’t know it was still being developed. That was the first DAW I had ever heard of as a young teenager.
Overall I think you’ll need to look at it like you’re composing, because you are - I had the same worries as you, but don’t worry about “passing” for original. Hookpad is only a small part of the equation and one of the tools in your toolkit that will hopefully be ever-expanding, and I can say it’s helped me learn a whole lot as well. (Such as that sketching in the DAW back in the day was a truly avoidable slog.)
Good luck, and have fun.
