I think that you will have difficulty every time you encounter officialdom. The good thing about the majority of the trip is that you can almost make a beeline from the Singapore straits to the Philippines. It could be wise to remain well offshore between Phuket and The Singapore Straits, although It is my understanding that Langkawi may be prepared to let you transit through the port without too much trouble. Friends of mine are currently in Malaysia and say the local officials are very helpful toward cruising yachties. But, check it out as that is heresay.
Of course the straits of Singapore are amongst the busiest seaways in the world and traffic entering or leaving is required to have both transmitting and receiving AIS. Once south of Malacca, I would very carefully plot my route through the Singapore Strait to ensure that I remain well and truly in international waters.
Dependent upon the reception from Langkawai authorities you could sail directly to Kota Kinabalu. During a similar trip I hopped along the coast of Borneo. But, the island is under control of Indonesia, Brunei and Malaysia and if I was considering landfall, it would be in Kota Kinabalu (Malaysia). From there, you just need to pick an entry point in the Philippines and hope entry is not to difficult. In pre Covid days, it wasn't too tedious, but that depends upon where you make entry.
The trip along the northern Borneo coastline is reasonably protected. I did it single handed in a 55' sloop. Night time passages, when closer to shore, were occasionally made difficult by unlit fishing nets, but that's par for the course in SE Asia.
It's a good trip and in my memory, the Malacca Straits, Singapore Straits and sailing into the Philippine archipelago required a heightened level of awareness. Being not permitted to drop anchor frequently due to Covid restrictions is a complication, but if it can't be avoided, the trip is certainly do-able during outside of the monsoon season.
A lot of sailors are currently holed up in various parts of the world due to quarantine restrictions. It's a complete pain, but it's better than being dead. Best wishes and please let us know how you get on.
"if at first you don't succeed....Redefine success"!