Ashley
It seems that C3 is still mostly unusable with source control on account of the .c3proj file and UID shuffling.
The .c3proj
If more than 1 collaborator adds a new behavior, effect, object type, family, layout, event sheet, script, or timeline, it modifies the .c3proj and creates a conflict. This might be the case with removing and renaming as well. This can be resolved by hand, but is obviously very error prone and can easily corrupt the project.
As it stands, all users except one must basically only touch existing contents.
I'm not the expert here but one potential solution that comes to mind is replacing the .c3proj entries with individual files and populating the project bar etc. from those instead (basic project properties can remain as one file). Each object already has its own .json file anyway so why not just extend this format to the aforementioned assets instead of making lists inside the .c3proj?
UID Shuffling
Furthermore, UID shuffling can be detrimental and risks breaking many things in your game or outright corrupting it. UIDs are the only auto-assigned reference that instances get which are identical in both the editor and runtime. They are often used extensively to manage objects in save data or managing connections between objects in and across layouts. The only alternative is manually-assigned instance variables but...imagine a Mario level with hundreds of coins per level or a Metroidvania with hundreds of items scattered throughout the world, each one given a manually assigned variable to prevent from respawning or what have you. That is just insane, but there are C3 users who are doing just that to prevent their objects' only real IDs from being scrambled.
Again, not the expert here, but sequential UIDs might not be the safest approach. I believe skymen had proposed some sort of UUID but he would need to elaborate on that.
Taking a quote from your GitHub tutorial: "Source control is widely regarded as mandatory for any kind of professional development." I strongly agree with this sentiment but as it stands even small teams cannot use C3 together with confidence. I see that improvements have been made over C2, we aren't quite there yet. If Construct 3 is to be viewed as professional software, especially with paid tiers and increasing prices, then its compatibility with source control needs to be locked in. Thank you for reading and I hope you give these issues your consideration.