for the ender/twilight portal backdoor it's not about having one in your base initially, it's that a player can fidn the right coordinates int he nether/twilight forest and make a portal THERE that spawns a portal inside your overworld base often eating important things inside at the same time. one of the youtubers, ako the builder i think, accidentally did this with a twilight portal and almost fried a bank of machines in his base in one episode. so to prevent them spawning a portal into your base you either need to also build a secure zone of matching coordinates in both of those dimensions, or build in a mystcraft age.
as to warded stone and mffs, use the defense stations. a field of warn at 16 from the wall action field, and an action kill field of 16 is two chunk radius in square mode around the wall of warning and then death. the field then becomes a matter of eating frame machines turtles and pistons that get coded or pulsed through the player death field(which afaik doesn't actually need a forcefield itself it's simply a region effect from the point of the defense stations placement, mffs documentation and videos that do more than read the gui's are kind of lacking). the block breaker field layer must be pulsed as frame machines can simply pass through static fields, even block breaker static fields, but by pulsing them on and off they WILL eat frame machines in their spawn locations. the problem of course is timing and system resources.
frame motors can move much faster than 1 block per .8 seconds if they use a stacked or caterpillar drive instead of an inchworm setup. about twice as fast actually, in bursts.
pulsing any reasonably large mffs field at .4 on/off is a huge system resource drain performance wise. my solution so far has involved making the field thicker and pulsing slower.
ideally at this point i believe one hits the point that it simply becomes far easier to build in a myst age and ensure that the possible entry point (say from someone stealing your linking or descriptive book) is secured instead of the entire structure, and use the defense station layering or command blocks to remove offending players who magically /tpx or otherwise access the secure age through other means.
securing things in minecraft is a LOT of work. trying to make a map in which all the goodies exist in secured structures spread about and thinking about how a player must break in to get them teaches quite a bit.
other stupid pet tricks that may or may not be valid at current patch levels.
mining laser in rp2 deployer.
gravity gun in rp2 deployer.
at one point gravity guns would dupe warded stone(one in gravity gun grip the original still in place).
secret rooms hidden blocks on warded stone crashing clients and servers(still seems to cause performance issues think it has a hard time when looking up what texture to use with also receiving the metadata on what player has rights on the warded stone and on some playernames causes a condition not expected by its handling logic).
the trapdoor logout teleport to the next open space above glitch(build at the minimum y height with walls straight up. to avoid).
chunkloader contention. too many chunklader types from more than one player on the same chunk can cause the system to derp and allow a chunk to unload when the later loaders are removed. theoretically could be used to frame move a portalgun portal in close enough to an unloaded base to pull some trickery. still don't understand how to cause it specifically.(also remember mffs blocks chunkload, and portalgun spawners while active chunkload as well.)
if they're using cc computers for security control, simply laying down a ton of them on and nearby can cause
theirs' to stop working. seems to be some kind of limit as to how many computers can be on at once in a region.
also if one can somehow get a copy of one of their named computers or turtles all kinds of undefined weirdness can be done, as the programs and data for each labeled machine is the same but the stuff while they are running differs. so two copies of a computer labeled "bob" obtained either through creative mode duplication or immibis duplicator for ease of reproduction. one is merrily running away automating something for them. you plop the copy down anywhere and fiddle with the saved programs. the original will use the old stuff to run from until it next reloads/restarts. interestingly if they rewrite anything on theirs your copy will receive those changes the next time the copy reloads/restarts. this is handy for adventure map use as a kind of magic modem method without range restrictions. it's also almost certainly a design oversight of computercraft. even weirder with cloned label turtles.
highspeed boosted items on tracks, when they fail to decelerate properly, explode in a small radius. sometimes this ignores the facts of warded stone/warded glass.(doesn't take the warded stuff out, but things on the other side of it.).
as to the solid walls/ender pearl/mps bit layer walls with gaps. a field jammer block breaker mffs field will happily ignore warded stone and glass, and also another mffs field fed by the same capacitor. warded stone>mffs pulsefield filled gap>warded stone>2nd field pulse gap>warded stone>rest of 2nd mffs field. they will land in either the outer fields regions or the inner fields regions and the defense station will get them, or the field popping into existence on top of them. whichever ticks faster.
very annoying to construct however, as fillers can't process warded stone in any mode at all. this leaves doing it by hand, or having a turtle lay the warded stuff down. i have yet to take an nbt editor look at what the blocks store when placed by turtles or work out who has removal permissions when they lay it. it's hard sorting out the per user permission based blocks when working alone.