I think the multi-layer Magnet is the only way. Without seeing an example, I can guess a couple of things that might affect its performance...
1. Check the tool's Radius setting. The tool has a fall-off so if the graphics points are limited, you may see what appears to be irregular movement. Increasing the radius should solve that.
2. Make sure your geometry supports the type of deformation you're trying to achieve. You might need to add more points to the curves to get them to deform predictably. Sticking to regular points vs. Bezier points can also have an impact.
I hadn't noticed a problem with the multi-layer tool mod but it's been a while since I last used it. When I get a chance to check it (maybe this evening after work,) and let you know what I find here. (I'm assuming you're using A.Evseeva's mod.)
BTW, there's another
Magnet mod by DKWRoot that allows you to switch between different fall-off modes like smooth, linear, spherical, etc. Unfortunately, this is a single layer tool. It would be cool if A.Evseeva could update their script to have similar fall-off options.
Actually, there are some workarounds without using a multi-layer magnet that I can think of...
1. One workaround would be to copy all the vectors to one layer, use the standard Magnet on them, and then send the modified curves back to their individual layers. If this sounds too clunky for you...
2. ...another workaround is to have all the shapes in one layer and then reference that layer for each additional layer you need. You can delete the unwanted shapes from each layer
but keep the curves (i.e., the non-rendering 'wireframes'.) Now when you use the Magnet tool on the curves in the
original layer, the shapes in the other layers will all update as if you used the Magnet tool there. This is probably the most reliable way to do this without using a multi-layer magnet.
Hope this helps.