Method might have advantages and... problems, depending on map-type, a simple map should not have any major issue. I could figure solution due to some zone leak occurred - as history.
Shortly, we might have some hole to pass which sometimes Editor will never link even if jumping is possible - high skilled Bots can pass such areas. Editor will be less cooperative making a Network split:
So building paths is not recommended in this case because of above issue. Now let's fool Editor - dare to open Spoiler,
As we know so far Editor will link nodes in a water zone doesn't matter how they are located - more or less on Z axis. Editor will never understand our lie, so later we can restore zone properties bWaterZone to original value - FALSE - after building paths with PATHS DEFINE command.
The random trouble.
Route to PathNode placed lower is simple reachable. If pawn is coming from a lower Node to a Higher located Node on a big box will have problems. For creating isolated links we can temporary set some WaterZones - cylinders or such, building map and paths, removing WaterZones, rebuilding map again WITHOUT to rebuild paths (UNCHECK PATH BUILDING BOX for safety in build menu - and use "manual driving"). If we do setting for entire Level, every link is debated like in water considering that pawn can move between points, so more links are expected. Go figure if situation is suitable for Non-water related to links created - should not be pickups in those spots if locations are higher than Pawn can jump else it will run in place trying to get items.
In current sample map I did not add any Inventory in Manta's room, so Bot will not move there as long as there is no purpose for roaming in that location - see nodes in game with ShowAll command.
Preventing to follow high route in such situation is doable with a node with bSpecialCost. In Event we can setup some condition for seeker - accepting bCanFly types and discarding them if not - a tiny coding is required for such task because stock doesn't have such "FlyPathNode" but it is doable and operational, engine working correctly in game.
Probing/testing is a MUST, for preventing a surprise. RememberSpot and ShowPaths are helpers here because... Bot will not fly to check these spots for you. You will use "Fly" cheat command before trying to find target spot. If WayBeacon is not shown, paths are borked (too close to walls, too far, etc.). Do not use helper commands in maps with WarpZoneMarkers and TranslocatorStart - you can crash the game, BotPack is BOT-PACK not HUMAN-PACK.
To summarize we have to do a simple setup temporary and then restoring it back. Is simple but it can go crazy if geometry has nasty higher spots which need paths. That's all, folks.