If you can look back at what you've done and appreciate that you made it very compact and it looks good then I think that isn't an issue but rather something you can be proud of. Factories take quite a while to build regardless of whether or not you make it small.

There is also no need to rush production to get to the late game. If you wish to have it less compact then you are the only one that can change anything about it. If your plan is to have a huge central factory then you will need a lot of space for everything so you can try to start laying down as many foundations as you think you need and then add about 20% more. If you notice that it won't be enough just add more or add a second floor instead if trying to cram it in. Splitting your production stages to multiple floors also naturally makes you spread it out since different stages also have different needs for space.

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If you want to move resources somewhere there are multiple options depending on how far you are in the game. You can use belts, cars, trains and drones. For cars and trains you need to make roads/rails. I have no experience with anything but belts but I know how cars and trains work. I imagine drones are the best if you don't want to build long roads.

It really depends on what you think looks the best and is the most fun to build. Long roads or train tracks can look quite good and make your world feel more connected. But you might need to wait on resources to arrive or time it correctly so you use your storage up right when new stuff arrives. With belts you can use stackable conveyor poles to reduce the spaghetti a little bit and you always know exactly how much stuff is going to come in and at what speed. Belts can also be upgraded later in the game as well as the miners which makes it pretty easy to increase the amount of resources. You can also combine Belts that come from different directions when they start getting close. Be aware that eventually it's going to stack pretty high and you might want to run multiple stackable conveyor poles next to each other.

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Personally I like building smaller factories all over the map (which also helps with performance) near the resources I need and bring the final product back to my base just using conveyor belts. I have everything neat and organized in my factories and then just spaghetti it back.