I'll offer suggestions based on my experiences with the house main sewer line and root clogs. I'm not cure whether these will work exactly with your situation of buried flexible downspout extensions, but much of it will.
Roots can and will sneak into any line with a regular source of water. They themselves can be the blockage, but they also become a filter net and fibre reinforcement medium for small other materials to collect.
A heavy-duty sewer auger (manual or motor-powered) designed for main sewer lines definitely to TOO rough for the flex stuff you have. The small in-house drain snake you linked to likely is not too tough. But it may or may not be strong enough to tackle a root ball. Maybe a small root bulld-up if it's not left for a long time. However, that small snake may be able to push through a root ball and open a small hole in the middle, but it will not cut out the majority of the clog.
A high-pressure hose system with the right nozzle to create jets out to the sides will do a decent job, but if the clog is already substantial you cannot do that from the top end. Wiork up from the discharge end so the material loosened can flow out of the pipe that's already cleared. For the home DIY person, a garden hose with a simple nozzle that can spray a single jet forward can do that job, too, although not completely.
Chemical treatments work only when used correctly. Here are a few pointers.
1. As you say, you don't want these chemicals to damage the garden plants, and that will be a problem. Copper metal, Copper Sulphate (a salt of Copper) crystals flushed down with water, and several other heavy metal salts are often recommended. All of these are toxic to some extent to plants and often are used (e.g. Copper Sulphate) because they dissolve easily in water and thus can spread throughout the pipe. But that also means they will be carried up throughout the plant and cause toxic damage everywhere. For trees, the extent of that damage usually is minimal and unnoticed. Not so sure about flowers, though!
2. All those things that can be carried along the pipe with water have one significant limitation. They tend to move only along the bottom of the pipe, and hence have their greatest effect on only the roots along the bottom.
3. You can NOT use chemicals to clean out a line already blocked with a root ball. The chemicals will only reach the upper end of the clog and attack the roots there, leaving the rest of the clog intact. Yoiu must physically un-clog the line first (auger, water jets, etc) so that the treatment can get through the whole pipe.
4. The best product I have found for my main sewer line and its tree roots is called Root-X. It comes in a plastic tub containing two chemical powders in separate compartments, and you should buy also their mixing funnel. The standard size is 2 pounds of powder, suitable for treating about 50 feet of 4" drain line. A larger container is available, but not suited to your needs. One powder is a chemical which is toxic to the roots, but does not easily get transported from the roots up into the tree and is supposed to be less toxic to the tree anyway. Thus it is supposed to damage only the roots it contacts in the pipe. That causes them to break down and rot over a short time so the slush can be flushed out by normal water flow. The other powder is a special foaming agent so that the mixture you flush down the sewer line completely fills the line for a while, meaning that ALL of the roots get contacted by the toxin. To use it on a house main sewer line you add it either at a sewer clean-out if you have one, or from a toilet close to the start of the line in the house. You need to get a pail and fill it with about 5 gal. of water to have ready. You screw the mixing funnel (with its cop cap in place) into the top of the plastic container and tumble this assembly a few times to mix the two dry powders. At the toilet you flush it and immediately pour the dry mixed powders into the water votex so they are flushed into the sewer line. Then you pour the extra 5 gal pail of water right after that, to ensure the mix gets pushed down the line. Then you must NOT put any more water down the line for several hours to let it do its job attacking the roots. After several hours the foam will have collapsed and you can resume normal use of the sewer line. I have used this product AFTER using a mechanical auger to rip out the main clog, and it kept that liine unclogged for a long time - much longer than just the auger operation had done before. The plan is you do this as a preventive measure about once a year BEFORE the new clog can block things up, and it will keep the line clog-free by removing roots before they take over. Another important application note for tree roots, anyway. When they are mechanically damaged by an auger, they will start immediately to protect their raw open wounds with their own chemicals. Thus the Root-X MUST be applied within minutes of the auger reaming operation. OR, if you can't do that, you must wait 6-8 weeks after the auger operation for new tender rootlets to grow, and THEN apply the Root-X so it can attack the entire root system via the new weak rootlets.
I am not sure exactly how you could adapt this to treating smaller roots in your smaller flex hose system. Certainly you would not put the entire 2 lb batch down one line, nor would you use further gallons of water to push the chemicals far down a short line. But you probably would pour some extra water down each line, just to prevent the developing foam from backling up out of the top end. And of course I do not know whether this chemical system is suitable to kill off the roots you have (they probably do include at least some tree roots), NOR whether or not these chemicals are likely to damage flowers, etc. For those questions you might try to contact the Root-X company and ask their advice.
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