The first reason these two types of machines work differently is a major one. DOT SIZE. Your dot size is many times larger on the galvo than you're used to on the gantry which has a couple of consequences.
For one, your 40w of power is spread out over a much wider area on the galvo thus your energy density is much lower. This means you are going to have to pump more power into the material to see the same ablation effects which will absolutely have an effect on the final result.
The second thing to be aware of with the larger dot size is that your rendering fidelity is going to be effected. You are going to struggle to resolve details in small areas and you're going to see faster heat build up than you normally would, especially in tight spaces.
Finally, be aware that your galvo laser is (very much likely to be) a pulsed laser. Pulsed lasers distribute power differently than continuous wave lasers. Continuous wave lasers in general distribute power more evenly, over time, and peak power distribution to the material tends to be lower than on a similarly powered pulsed laser (RF Tubes, generally). The pulsed laser output is pulsed because it allows the laser to charge bursts of energy between pulses to provide more “punch per pulse” than would be available from a laser that is distributed as a continuous wave. (DC power output from glass tube laser sources in terms of cutting when compared to RF tubes commonly found on galvo lasers is a separate topic and is only marginally related, but I won't get into it here). This inherent difference in beam generation is going to result in discrepancies between the two machines, for obvious reasons.
So what's the answer for this particular application? There's no cut and dry answer unfortunately. Reading back on the notes above and trying to reduce the symptoms of these discrepancies would be a good start. The machines will always be different at their core so there's no use in attempting to change that.
Since you have a lower energy density from your enlarged dot size, it would be worth it to attempt to bring that dot size down. You won't achieve parity with the gantry laser but you can almost certainly do better via a few avenues. Before we dive into them there are a few important things to understand. Due to the nature of F-Theta lenses it's important to grasp that the larger of the diameter of the beam going IN to the F-Theta lens, the smaller it exits. It's weird, I don't know - chalk it up to physics - that's how it works. With that in mind what we are trying to achieve here is the LARGEST BEAM DIAMETER BEFORE THE LASER ENTERS THE F-THETA LENS. It's counter intuitive, don't think about it too hard. With this understood lets take a look at your options.
1. Use the SMALLEST lens field size you can for the work. Reducing the lens size will likely be one of the most easy to see improvements to your work and it's simple and relatively inexpensive to accomplish. If you don't have a wide range of lenses for this laser, pick up a few - it's a worthwhile investment as you'll discover quickly when wandering away from processing the “standard” materials.
2. Use a higher magnification beam expander. This is a complicated topic but we cover it fairly well in this laser everything episode Everything You Need to Know About Galvo Lasers. (1. below) Make sure not to use an expander that makes your beam too large for the mirrors in your scan head. Which brings me to the final suggestion for dot size.
3. Increase the size of your scan head. While many newer CO2 galvo units are shipping with 20mm scan heads a majority of them do not. 10mm scan heads severely reduce the magnification maximum of the beam expander, which keeps your dot size large. Upgrading the scan head will allow you to use a higher magnification beam expander. Larger beam in, smaller beam out.
The key here is trying to create an even distribution of energy along marked area which can be rather difficult and will require a little math to get right. Since we're trying to mimic the effects of a continuous wave laser our goal her is to get the pulsed laser's [duty cycle] as close to 100% as possible to reduce fluctuation. We won't get to into it here, but the short and sweet is your laser is ON for a certain percentage of time while pulsing and OFF for a certain percentage of time while charging. A 100% duty cycle, a laser that is always ON when active, is continuous wave.
Do not confuse [duty cycle] with laser activation. If your laser software tells your laser to activate while marking an area and then deactivate to skip an area that should not be marked, this is irrelevant to duty cycle. Duty cycle refers directly to the amount of time the laser is ON DURING PERIODS OF ACTIVATION. A key distinction!
Note: some CO2 RF tubes are capable of continuous wave modes. You'll have to consult your manufacturer or reach out for help in one of our communities to get a definitive answer on this and find out how to activate continuous wave mode on your specific make and model of laser tube. If your tube IS capable of continuous wave, activating it will resolve this discrepancy and you can go on about your day. If not, keep reading to learn more about how to do your best to emulate continuous wave with a pulsed laser.